I don't have any difficulty believing that the aldehyde is unstable - Stuart Warren once described aldehydes as "barely on the verge of existence"... so yeah, make it and use it.
Since you're not getting mass-balance out of your reactions there must be an issue with the work up - maybe hemiacetal formation which then sits in the aqueous layer? How do the reactions look by TLC prior to the addition of anything aqueous? Can you just pass the reaction mixture over a plug of silica or something, rather than doing an aqueous workup?
I think MnO2 only works for allylic/benzylic alcohols, although maybe MnO2 on carbon is different.
Other oxidations to try: TPAP, TEMPO/BAIB or TEMPO/bleach, PDC (should be milder than PCC), Oppenauer.
Good luck!