I've encountered this same ProSeries issue before. 990-T e-filing does not cooperate with Form 3800, and will produce errors regardless if you attach it as a PDF or not.

In all honesty, the easiest ways I've handled this is to do either of the following:

1. Either turn off the error checking and e-file it anyway (the ProSeries way).
2. Or just paper file the return with 3800 and 3468 attached—much less aggravation.

Although the IRS instructions for Form 3800 are quite clear on handling these credits and attachments, it is worth reminding you to take a quick look (IRS Form 3800 Instructions).