As the developer of FlashFXP, I don't use linux or wine and I'm not very familiar with either of them. I've heard feedback from linux users who inform me that the compatibility problems with wine are due to limitations in wine.
If there was a way I could work with them to improve support I would but I don't see how I'd be very useful. I heard that WineEx improves compatiblity in some areas while lacking compatiblity in other areas where wine works perfectly. I think if all the wine projects were to merge their code then FlashFXP would work perfectly but I don't see that happening.
FlashFXP v2.1 seems to work much better with wine, in v3.0 we started using virtual list views and I believe wine has some compatibility issues with them.
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