Had a creaking i narrowed down to dry crank/bb threads so i pulled em, cleaned em up and regreased all the threads. reinstalled and noticed an increase in resistance. i backed off the non drive side cup a tiny smidge, which helped a bit, but still there's a bit more than there was at the start.
there's no roughness or grinding, the bearings seem smooth enough, but if i give the cranks a good spin with chain off they spin maybe once around and stop.
i know i need to abandon the isis setup eventually but should i sweat it now?
I have the same issue and posted on this a couple of weeks back. There was no consensus. If the search function is working, check out my post.
My situation is very similar to yours:
Truvative Gigapipe SL installed by LBS about six months ago.
I was stripping the drivetrain down and noticed the BB had lots of drag - smooth action, but hard to turn. Almost to the point of hurting my fingers on the ISIS splines when trying to spin the spindle
I removed the BB and the spindle spun freely and had the feel of a well greased BB.
After I installed the BB, the drag on the spindle increased. Like you, I found it was somewhat related to the installation torque on the cups. The BB said to tighten the cups to 25-30 ft-lb (which I did). Still had the drag feel, but not as bad as it was originally. It's a smooth feel (no grinding) but just hard to turn.
Bottom line - I torqued them to 25 ft-lb, replaced the components and I don't worry about it anymore.
update after a couple hours on the road, creak/clicking is gone, which is what i was chasing to start. the bb drag seems to have loosened up a bit, but still it seems a bit stiff. i can't say i notice any ill effects while riding but it kinda bugs me knowing how freely my other set ups spin. might have to drag it over to my trusted mechanic for another opinion.