I had this issue with an infrequently visited beacon on phem, it was giving me warning but my gc definitely covered it. Thing is, i fueled the beacon prior to getting gleam club. I left it to “burn out” according to the warning, then visited it after and havent had a msg since.
I cant be sure, but the warning is possibly due to the game picking up that my fuel that i had placed was running out, regardless of my gc time. Once the fuel was gone, the game had no timer to go on other than my subscription, and subsequently straightened up and flew right.
Dunno, but may be worth investigating. Will be at least a 4week experiment though 
unless a dev wants to chip in with coding info 