Are you suggesting I should connect the Modfactor as a Master and the Timefactor as a Slave, midi-wise ?
No, it sounded to me that you were running MF into TF (your signal chain). Try TF into MF, I think that will solve the problem. Sorry if I sounded abrupt, I'm genuinely in the middle of a frantic trauma, wish I had more time to think it through (I'm not sure about the midi stuff here). Anyway, give it a go.