Why do some counties have more "uncounted" votes than others?

Short answer:

The lack of standards took their toll on election night, when Florida's six million plus voters cast their ballots on different types of ballots and had them counted by different types of machines.  As it turns out, the system through which more than 60% of the votes were cast, the infamous punch card system, accounted for more than 80% of all the uncountable ballots (uncountable by machine anyway).  Since Gore handily won the majority of votes cast on these ballots, it is likely that he has more votes among the many uncounted punch card ballots.  The system through which about 35% of Floridians cast their votes, scan ballots read at the precinct, accounted for only 10% of all the uncountable ballots (uncountable by machine anyway).  Bush won the majority of votes cast on this highly accurate system.  Much of the remaining percentage of both counted and uncounted ballots were on a third system - scan ballots read at a centralized location.  These ballots went heavily to
Bush.  Since this system had the highest “lost vote” rate of the three, Bush likely lost more votes than Gore in these counties.  However, this system only registered roughly 16,000 uncounted ballots, while the punch card system registered between 140,000 and 150,000.  Moreover, many of the counties using this system were among the handful that conducted manual  inspections of their "lost ballots" to determine the "intent of the voter" during the original "recount."  None of the counties
using the punch card system conducted manual recounts during the original recount.  How is that possible? Because what constituted a fair and accurate recount varied from county to county.

Click here for story from Orlando Sentinel confirming this analysis.

Long answer:

Of Florida's more than 6 million votes cast on election night, nearly 180,000 went uncounted because they were either blank or spoiled (i.e., voter error or machine reading error). That total is about 3% of all votes cast.

Roughly 5.8 million ballots for Gore and Bush were counted on election night, and less than half of those ballots were recounted during the official recount according to news reports.

http://www.latimes.com/news/nation/20001115/t000109544.html

Florida has three primary types of voting systems consisting of two basic ballot types.  The first ballot type is the scan ballot, on which the voter darkens in blanks to indicate preferences much like a scantron test.  The other ballot is the punch card, on which voters punch out holes to indicate preferences.  Those two ballots are employed by three basic voting systems.

1) Punch card system -- This is the most common system in Florida and also happens to be the most unreliable.  Many of these machines are about three decades old.  Experts estimate that the average uncounted rate for this system is about 3-4%.  That means for every 100 votes, about 3 don't get counted by the machines because the chads don't come off or the voters double punch or no whole is punched.

 http://www.nytimes.com/2000/11/17/politics/17MACH.html

Of the roughly 5.8 million votes counted for Gore or Bush statewide, roughly 62% or 3.6 million were counted by the punch card system.  Gore won 1.9 million of these punch card votes (roughly 53%) and Bush won about 1.7 million (about 47%).
Now here is the kicker -- of those 180,000 ballots never counted, 150,000 (83% of uncounted ballots) are from counties using the punch card system.  These counties had an average uncounted rate of 4.6%.  According to voting experts (including voting officials and the folks who build the machines), the only way to recover any of these uncounted ballots is to count them by hand.  This is standard operating procedure in close elections across the country.  However, not a single one of these uncounted ballots has been counted by hand in Florida.  This means that tens of thousands of Florida ballots have votes on them for both candidates, but have never been counted -- not on election night, not during the so-called "recount," and not ever if the Bush campaign and Secretary of State Harris have anything to say about it. Roughly half of all the punch card ballots counted in the state come from three counties: Broward, Dade, and Palm Beach.  Roughly half of all the uncounted punch card ballots in the state come from those three counties.  Does it come as a surprise then that Bush opposes manual recounts in Florida even though one is occurring right now in his own state, which is using the same guidelines as the ones in South Florida.

http://www.nytimes.com/2000/11/13/politics/13COUN.html
http://www.washingtonpost.com/wp-srv/onpolitics/elections/texas18.htm

2) Optical Scan with precinct reads -- This system uses the scan ballots, is the next most common, and is the most expensive.  It is also considered by experts to be the most reliable of the three used in Florida.  It consists of scan ballots and at-precinct reads.  Some of these systems scan the ballot immediately and spit it out ballots with errors  for the voter to correct them.

Of the roughly 5.8 million votes counted for Gore and Bush statewide, roughly 31% or 1.8 million were counted on this system.  Gore won roughly 830,000 (46%) of these votes counted and Bush won about 982,000 (54%).  Here is the next
kicker -- of those 180,000  ballots never counted, only  15,000 (about 8% of all uncounted ballots) were in counties using this highly accurate system.  These counties had an average uncounted rate of about 1%, which means that voters casting ballots in this system (the majority of them Bush supporters) had the highest number of their votes actually counted.  Of the 10 counties that conducted hand recounts (7 of which were in counties won by Bush), 4 of those were counties that used this most reliable system.

3) Optical Scan taken to central processing areas -- Although highly uncommon, the reliability of this system varies.  Ballots are not read at the precinct and voters are not automatically alerted to ballot errors.

Of the roughly 5.8 million votes counted for Gore and Bush statewide, only 6% or 360,000 were counted on this system.  Gore won roughly 160,000 (45%) of these votes counted and Bush won about 200,000 (56%).  Here is a third kicker -- of
those 180,000 ballots never counted, 13,000 (about 7%  of all uncounted ballots) were in counties using this system.  These counties had the highest average uncounted rate.  That suggests that the small number of voters casting ballots on these machines (the majority of them Bush supporters) were the least likely to have their votes counted.  However, of the 10 counties that conducted hand recounts, 6 of those were counties using this system; 5 of those 6 counties were carried by Bush. Since more than half of all the votes cast on this system were included in manual recounts, many of their uncounted votes on election night will be included in the final vote tally.