I have in the past changed ownership on all scripts to public user, and pulled back over. The problem re-occurred unfortunately.
As far as #2, we see the same thing as well. The trouble being with this is we have quite a few scripts and it can get hap hazard to constantly monitor, and rebuild as needed although it works.
For now I have mitigated by making all script changes on the core. This works around the issue. I just never remember having a problem with V9.0. Strange.
Thanks for the info though!