What linux distro and wine version do you have installed? You are talking about the linux version of tracktion and using airwave with it?
Iirc you have to use a wine version that has a certain patch activated (xembed protocol) for being able to use the gui functions. Maybe this is your problem, and tracktion handles something different working around the problem? Normally the vst guis should look just like the native plugins.
I had quite good results with the wine-rt from kxstudio. I seldom use it though, as I'm trying to keep on to more stable native stuff. Well - this wine version was probably configured with audio and vst bridging in mind. Some plugins can freeze my vst host though after a random time of usage (this can happen with some programs I run under that wine and load these vsts too, and also with other wine versions from different sources). The others load a bit slow and perform suboptimal in terms of cpu usage. But renoise will load their guis via airwave for me.
As for plugin scanning, yers, I also remember some plugs are very slow loading, some even crashing when trying to scan them, and many also resulting in xruns when opening/loading them, even when they are just scanned. This slow loading is also happening for the first time renoise scans them, afterwards it should use a faster, cached scan method. You can "debug" what is happening by deleting the plugin cache .db file(s) in the renoise settings folder to force a full rescan, and then watch the airwave manager lower window part with log level set to "debug" for all plugins or so, and the renoise status bar and log for which plugins are the bad boys.