In Dev 29:12 in the word Hayom is the kadma on the Ha or on the Yom? TropeTrainer is ambiguous and I don't have a Tikkun handy. I think it might be a sneaky case of nasog achor because Lo is a one syllable word.
Actually, I am looking at my print out of the Trope Trainer (overall, I like it - so much easier to shlep a few sheets during my daily commute), and the kadma is at the very end of the letter heh, just before the yud of the word yom. The correct pronunciation is as you suspected - on the 2nd syllable - yom. If you placed in on the 1st syllable, it may sound like a question (the "Heh Hashe'ela concept), which is not the idea, here.
I can see where you would get confused. While Trope trainer is usually accurate, I have seen various errors crop up. I noticed that some things may also depend on your printer translating some fonts and such. For example, a Kri / Ktiv problem appears as giant bold letters on my HP 6700 printer. My previous HP 4775 printer didn't do this. (Go figure! I may email the Trope trainer author / developer and ask him about this problem.) I also noticed that sometimes, in the Tikkun column, the letters get squeezed, so sometimes I can't tell where words really end. Fortunately, after laining for so long, I have pretty much memorized the Torah, so I can figure it out. But, I can see where a novice can get confused - not that I'm suggesting that you're a novice :-)
Re the "nasog achor" - interesting theory, and I have to review the rules, again. But, I noticed that there is a psik between "hayom" and "lo" - something I don't expect, here. I wonder if the reason for that psik is to "cancel" the nasog achor?