Portamento as a continuous controller is rarely used - portamento is usually a feature of the synth you are using. My best guess would be you are quantising the start note/end note crossover. I have a couple where if there is a tiny gap between notes there is no portamento but if they overlap, even slightly, the note slides up or down. If you look in the editor, can you see overlaps? Sometimes your usual setting could be to auto quantise them, removing the overlap when you record. Artificially create some overlaps and see what happens.
