I have had no problems as well - just booked a dirt cheap SFO-SIN milage run for this month. Total fare was lowest UA offered on this run - $608. UA did not bat an eye when I told them I wanted to use systemwide upgrades.

There are certain efares that specifically say "no upgrades", but those are usually VERY low fares to KIX, TPE or other lower traffic asian destinations. If you need to upgrade on those routes, just buy the non e-fare (should not be too much higher than the e-fare) and you shoild not have a problem.

Good luck!