So after hours of fiddling: I found that
1.The Phoenix and or my pc may not like certain SD card type/brands. Or at least putting system/core files on them
2. I put the core and service pack on the same SD card as my 2600 roms and it updated no problem
3. Maybe too, its best not to uninstall cores, but rather simply to update and replace with the latest one.
I hope this helps someone else who may have this issue.
BIG SHOUT OUT to Bmack as he spent a lot of time helping me,
Tim