From the OP, .....
"I have a valid re-entry permit. Any issues inbound?"
He is asking about any issues flying to (inbound) to Thailand.
Answer ...as he has a reentry permit an onward flight not required by airline at departure or immigration on arrival.
You are incorrect regards obtaining a reentry permit from a non O single entry 90 day permission of stay.
You can obtain a reentry permit to enable trip out/return during the 90 days.