PokerTracker

I play on UB.

The HUD will sometimes show the correct number of hands, for example 12,572 for a certain player (I datamine). However, on another table that I have open at the same time it will show a limited number of hands for the same player (maybe something like 43). I can't take a screenshot, but I'm positive that they're the same player. There isn't any pattern to the player names as far as I know. Maybe the software isn't trimming surrounding spaces in some cases or something. It happens every time I play, and it's really not acceptable as it can lose me a good bit of money.

Thanks.

That sort of behaviour can be caused by your filters, for instance the Player Ranges if you see a player at a table with a different number of players or 'show stats from current limit only' if you see a player at a different limit.
Have a look at Options > Preferences and see how your filters are set.

Ah, I think I know what the problem is. Sometimes I play UB's 72 tables, which PT treats as a separate limit. Also, there are ante tables that it treats as a separate limit. Is there a way that I can tell PT to treat all limits of a certain level as one limit?

No, each limit name is treated separately - there is no way to count all "equivalent" limits the same. (Other than disabling the option so that all of a players hands are used from all limits.)
People should play differently at different types of tables anyway - different strategies apply when the conditions change, such as adding antes or jackpot contributions. (Of course, whether people DO play differently in different situations is another matter..)