I can help troubleshooting further, I have only loaded Accelerated Mana Regen version not sure, gamergate download, never patched...
It hasn't happened in like 6 hours with a new paladin but as soon as I used my restarted mage my mana jumped twice in 30 mins! The only difference I can think is as a new paladin I never use the mana refll effect (hovering over the clock) but as a mage I'm too impatient waiting for my mana to refill. So it seems to be related to the refill effect, can you guys/girls confirm?