Mixing v1.3.7 and v1.3.8 code together on the same site is dangerous ... and will definitely cause your orders to not be saved completely.
Instead of blaming the code, I'd be more inclined to blame an incomplete upgrade.
Try setting up a fresh install of v1.3.8a in another folder+database and test some PayPal transactions. You'll likely find that it works just fine. Thus, if your upgraded site isn't working, then you've missed something during the upgrade.
Surely you did a test upgrade on a test copy of your site, and didn't upgrade your live site directly without a test first?



