Ok me and my friend did some testing today about claiming flags.
I've left company and tried to take over his flags. And guess what? I could instnatly, without 72 hours waiting, place my flags and start claiming his when he left to another area.
What i could not take over were my 2 flags (which were placed before entering company, but after leaving it they stayed in company ownership). These are my only 2 flags in whole game and when i tried to place claim near them i recived info about recent upkeep, it was in seconds and was -18600 and it was rising to higher negative values (maybe it'll "rise" to negative value which corresponds to 72 hours). My friend placed a lot more flags and almost all of them had no upkeep, so i could instantly start claiming them. But there were also 2 of his flags that i couldn't take over. Those were flags that he placed as last ones.
Mu guess: This looks like limit of 2 plags per character is on and only last 2 flags placed are protected by 72 hours upkeep. Any new flag placed removes upkeep from previous flags, so that only 2 flags can be protected by upkeep.