I had what sounds similar to this last summer. I'd had it happen quite often after the remap, say in the M6 it would randomly struggle cruising at 80mph especially on a bit of an incline, so I'd have to drop it down a gear. Happened big tIme coming back from the New Forest up the M3 and then around the M25 where M4/m40 junctions are, so I was panicking big time as there's not really anywhere to pull over so easily and it was packed traffic. Mine was very heavy shuddering through the whole car really, honestly felt like the car was going to explode. I could partially rectify it by dropping down gears, but I had to get the revs to a real narrow sweet spot. It simmered down by time I'd got to the M1 junction. My remap highlighted that the clutch was slipping and this motorway episode made me get it sorted straight away.
So I got the clutch and CV spiders replaced and all has been fine since.
Could be something totally different for you though.
GT 3.2 V6 - Q2, KONI FSD & EIBACH PROKIT, GTA REMAP, MICHELLIN PS3's, BMC CDA
159 SW 2.4JTDM TI - ALFATUNED, WIZARD BACK BOXES, KW V3 COILOVERS, NOKIAN WR A3/MICHELLIN PS3, PCA DYNAMICS ALIGNMENT.