The "6-hour-problem" is not ony an issue with egate entry, but also with normal stamp entry.

A talkative border officer once explained to me that they process entry/exit information in "batch mode" four times a day. So, in the worst case, you enter just after a batch run and run into issues when leaving within six hours.

The situations I had:
(1) EGate entry/exit: The border officer "clicked it away", but my card was afterwards screwed and had to be reset
(2) Dubaian stamp entry/exit: You need to find the right entry-stamp in your passport (a challenge in mine) and produce evidence you entered (keep your flight stub from the inbound flight!!!). Border guys take a photocopy of stub and passport stamp, and supposedly somebody is manually exiting you once batch run occurred. Personal experience: On next reentry into Dubai you are told "you never exited" because nobody really processed the exit.
(3) Abu Dhabi entry, Dubai exit within 6 hours: Good luck to anyone who tries. Did it multiple times myself now, and it easily takes 30 mins at the Dubai border post (with lots of phone calls and required documentation). After 30 mins they still do not figure out what is going on and just stamp your passport because they are sick of looking for the correct solution.