This started when FlashFXP turned into using "virtual list view", this was around version 3.0 to make the listing much faster. Since then all versions of winex/cedega/wine have huge problems with listing directories. The glitch you describe can get away if you turn to local view and back to remote view on both panels. I'd really like to see some improvements on the wine development to resolve this issue, but so far nothing happened AFAIK.
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