I've been playing with the Alienz a little, and I've determined a few things that might help fix the bugs. I'll add to this when I find more.

1) The reloading issue only happens with the MX and Katiba series of weapons, as far as I can tell. I haven't tested with the AAF's rifle, but I was able to play a full game of ION (from the reaction forces DLC) against Zetaborn with no problems.

Update: I used the 'CTRG Faction' mod, which uses the MX series of weapons, and there were no issues with the reloading. Perhaps the problem is not with specific weapons, but with the vanilla factions?

2) The Bloodseeker units show up as OFPOR, resulting in the rest of the aliens friendly-firing them. Perhaps you could take them out of the mod until a proper fix is possible?