Suspending my mercenary will not always pause the timer at the time I've suspended it. I've seen me suspend my mercenary with at 6 minutes left on the timer and as soon as I suspend it, it drops the timer to 0. I have a screenshot that shows that I just paid for my mercenary as I suspended it and it dropped the timer to 1m 59s. I noticed this across most all of the characters that I play regularly on this account.
This is a built in mechanic that seems to happen if your unsuspending and suspending too fast or within a certain amount of time. I suspect its to keep folks from "working" when the merc charges. Not sure what the exact timing is on this but it happens to everyone. I try not to suspend or unsuspend to close to when I last did it. If you go passive then it will cycle thru and charge you one more time for the 15 minutes so watch for that (this is what I think they are keeping everyone from blocking by having them charge if you do it too fast) Wait until they are 260 plat every 15 minutes...that hurts.