Even if some coworker had a grudge or a bone to pick with OP, they had to know that OP would return eventually and any CEO worth his salt would demand answers immediately. Specially considering the legal risks exposed here for firing someone on FMLA qualifying leave (assuming US).
Weigh that against a CEO who accepted a resignation and re-hired for the position based on a single email alone without so much as a follow up call. When OP returns seems lackadaisical about investigating. Seems fishy to me.