2 iTunes Accts. App Updating issues

I have 2 different iTunes Accounts associated with my iPod Touch, both with apps installed. Whenever I try to update any of my apps (even if they were not purchased with the first account) the password prompt for the first account pops up, with the prompt for the second one never showing. I end up having to delete my apps, and reinstalling them where the password prompt does show up. When I do that all my data disappears and it gets really annoying.
By the way, updating with iTunes isn't a solution. Since I run Linux which Apple COMPLETELY IGNORES, there is no iTunes for me.

anyone?

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