Some apps no longer sync to phone but appear on iTunes

I recently did a reinstall of windows on my laptop. After reinstalling apps and such, I noticed that not all of my apps synced back onto the phone. I checked every box and they show up on the right side where I can drag them from page to page, but they are NOT on the phone. It's about 20 of 50 apps or so. 3 I paid for, the rest are free apps. Some were downloaded from itunes, some directly to the phone. I tried removing all apps and then putting them all back on but the same apps refuse to sync, no matter what page the land on.
I know I can re-download the free ones but I would like to get the paid ones back without paying again.
Any clues?
Phone is jailbroken, OS 3.1.2 iTunes version 9.1.1.12

sounds like the appleID are set to different ones in the ipad vs. the itunes program on the computer

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