Innovative recommends not using the ground connection on the rpm cable so try lifting that wire off and see what it does. On my car, with the power wiring run as I have it, there is a 0.20 V offset between the ecm ground and the LM1 ground. Go into the setup for the tps channel with the key on, engine off, and both logworks and direct scan running. See what ds says for tps, then set that voltage in the lm1 setup and use the right click to assign that voltage to the current reading. Then floor the gas pedal, hold it til everything is rock steady on ds, and repeat for the other end of the scale in the lm1 setup. I have something like -.2 V = 0 V displayed and 4.7 V = 4.8 V displayed, and now over the full range of idle to wot both ds and logworks agree. You can do the same for the map signal - one point is easy, key on engine off is 1 bar or 14.5 psia. I teed a bicycle tire pump into my boost gauge and map sensor line and pumped it up to about 28 psig to set the upper point. Don't know anything you can do about the rpm offset but ungrounding the rpm converter might help.
If you or anyone else wants to go over this stuff in person at Cecil Co. in October I'd be happy to show my setup and help with yours.