I tried a post before but I'm not sure if it went through, so this may be a repeat.
I'm using both a TimeFactor and ModFactor with a Mesa RoadKing and using the effects in the loops without any problems. Am also new to the Eventide pedals but have a few things worked out. Couple of things to try. First check that you set the Input and Output level switches on the back of the TimeFactor to line level. Out of the box they are set to Guitar and Amp respectively and need to be changed when you put it into the loop. If they are ok, then I'd try changing the KillDry setting and see if that helps. If no difference there, then have a look through your manual for the unit – there is a process there for checking the input level into the stompbox. If thats ok, try reducing that output level and see if thats perhaps too high and overdriving the loop stage. Would like to hear how those things go for you. Hope they assist.