If you turn Partial file sharing off at any stage, LW's preferences will lose track of those files, thus even if you turn it back on 10 mins later they will eventually become red.

I presume your partial file sharing is turned on right?

Other than that I'm not sure why that would happen. But why are you using the Resume function if the incomplete files are already in the download window ... or were they missing from the download window? It'd be my guess incomplete files that did not show in download window & were resumed from incomplete folder would not be capable of partial file sharing (might be wrong.) The process might have temporarily tricked LW.

What sort of changes did you make?