I don't really my the continuity problems from 'Regeneration'. Mostly because I consider the ENT timeline to be an AU created from the effects of FC. Time travel was used to rewrite established history. Similar to what we see in ST09 with Nero and Spock.
I have no problem with "Regeneration" either, but I have the opposite interpretation: ENT is not an alternate timeline, and this episode simply established a closed time loop. The reason the Borg cube in "Q Who" was already headed in the general direction of Earth? They picked up the signal which the "Regeneration" Borg sent.