Nope, that's not it. Cambodian customs at Poipet have been a problem for Thai registered private vehicles for years. You see, Cambodia and Thailand only share an agreement covering buses and trucks, which enter and exit Poipet in their dozens daily (especially trucks), but there is no agreement covering cars or motorcycles since the Cambodian side is dragging their feet on this issue for some unknown reason. Exiting Cambodia at Poi Pet for Thailand is no problem, I've done it.
Nowadays, Cambodian vehicles can still enter Thailand under the new rules without making pre-arrangements, provided they do not leave the border province entered and return back through the same border they entered. The law has always been like this for Cambodian vehicles, since the Cambodians have the same rule in place for Thai vehicles, just that it wasn't enforced until June 27, 2016. It appears that some Cambodian vehicles are still "slipping through the net" and leaving the border province entered without permission since I have seen Cambodian cars and one motorcycle driving in various parts of Thailand over the past few months, including a few weeks ago in Tak province where I spotted a Phnom Penh plate heading north on the Mae Sot-Mae Sariang road. This will continue as long as the Thai police are not actively stopping these vehicles, despite checkpoints in places like Trat province where you have as many as 4 checkpoints between the border and the Chanthaburi provincial boundary. Customs are however enforcing the return through the same border checkpoint rule for Cambodian vehicles unless they have a permit. It could be that they will crack down especially once the new guide rule goes into effect in March, as I've been reading about recently but since the new rules have gone into effect it's still largely business as usual at the Thai-Cambodian borders as far as local vehicles are concerned.
The only two border crossings that definitely work for private Thai vehicles (or indeed, any foreign registrations) without needing advance permission from Phnom Penh are Chong Chom/O'Smach and Hat Lek (Khlong Yai)/Koh Kong. The latter will probably tell you that you can't leave the province with your vehicle but in reality there is nothing stopping you - I've done it. Leaving Cambodia is fine at any crossing though Chong Sa Ngam/Anlong Veng is a bit uncertain since some reports suggest that vehicles can't cross there at all, in any direction not even for local travel, while others claim that permission was granted but only for travel as far as Siem Reap. Exiting at Poipet, Pailin (Pong Nam Ron) is OK while Ban Laem should be OK but is also a maybe.