I think I have my similar to Bulgakov's issue solved too.
Last week i was on a travel. Total pictures: 1300. Cards used: actual CFs 32GB, 2Gb, 512MB. No CF to SD adapter used. No corrupted files. I tested slow & fast burst shots. All ok.
I conclude the corruption was caused by the adapter. The adapter I used previously was exactly this: http://www.amazon.com/SD-CF-II-Type-Adapter-Supports/dp/B000YZGCIU . I used with different SDs & had corrupted files aleatory with all of them. I don't know if other adapters can corrupt files too, but I think this does. Be careful.
I will invest in actual CFs and I will forget SDs and adaptors with my D300.
Thank you to Bulgakov for his post and to all that helped with this issue that has solved mine too.