OK, i think i figured my problem, it was the amount i was setting for my fuel, in a forum post in my research to attempt to figure this out before asking.
I had read that the amount is divided between the engines so i was doubling my fuel amount in the ST-settings and because with big bags solid fuel stacks to 500, so i guess the reason it wasn't being removed because it didn't meet the (max) set requirement (min 1250 = 50 solid) and (max 75000 = 3000 solid) which is 3 stacks per engine. Now that i have it set as an amount for a single engine it seems to be working fine now.
Thank you for your reply and your awesome mods :)