I brought my GP into the brake shop so they could finally diagnose the ABS light I've been getting. But, they told me that my car wouldn't re-start, and they had to put the battery on a charger. On the drive out of the shop, My 1-2 and 2-3 shifts were abysmally slow and soft (as in 2-3 seconds to complete a shift), but it went away after a while.

Same story yesterday: my battery gave out after a lot of short drives, and after a jump start, my transmission was acting up again. But, after 25 miles or so, the shifts were nice, quick, and smooth again.

Is transmission line pressure one of those "drivability" things that disappears when your battery runs down?

The Transmission Control Module (if the '99GP is so equipped) has to "relearn" everytime the battery goes dead or unhooked. Hopefully that is the issue here.

John'* right. Every time the battery is disconnected or "goes dead" the PCM/BCM/(TCM if applicable) has to go through a relearn process. You may even notice the car seems more "peppier" than normal, downside is, less MPG, but it will recover once the PCM relearns the engine.

I figured as much. At least the PCM can still correct these long shifts. Probably wouldn't hurt to get a new transmission filter installed with my next fluid change.