Thanks for reporting!
Regarding to Bug #1, this somehow happens in the following situation: 1) a new param. definition is created as "one layer adjustable and other tied" and 2) a second param. def. is created and tied to the first group. PEST tool complains that you cannot tied parameter to another existing tied param, which is correct! FePEST manages to create the parameters and groups properly at the beginning. But if you edit any parameter, the groups are somehow recreated not fully correct.
Solution: You correct manually the tied parameter(s) (from group 2) by tidying up to another parameter, which is not being "adjustable" / "calibrable" (from group 1).
If you need more details, support team (mike.de@dhigroup.com) is aware of the problematic and has some workarounds.
Apologizes for the inconvenience. We are planning a correction in the next update.
Happy new year!
Carlos Rivera