Helium 3.0
Helium 3.0 causes the Kaleidoscope control panel to crash when you select a popup menu. Tiger Technologies has fixed this problem in Helium 3.1.

Suitcase 2.1.4
Suitcase 2.1.4 can cause serious problems with Kaleidoscope, and if you want to use it, you must make Suitcase load after Kaleidoscope. To do this, put the Suitcase 2.1.4 extension in your Control Panels folder (it will work just as well there as it does in the Extensions folder, except that will no longer conflict with Kaleidoscope). Suitcase 3.0 does not have these problems with Kaleidoscope, and I recommend that Suitcase 2.1.4 users upgrade to version 3.0.

SmartScroll
To use SmartScroll with Kaleidoscope, you must have SmartScroll version 2.03 or higher. You can get the latest version of SmartScroll from Marc Moini's home page: http://www.kagi.com/authors/marc/ .

Retrospect 3.0, SiteMill
When the Substitute System Font feature is enabled, Retrospect 3.0 and some versions of SiteMill put up a font warning box. There really is no problem, and both Retrospect 3.0 and SiteMill continue to work normally once you dismiss this box. Please note that this problem happens only when Retrospect is launched manually, so it does NOT prevent Retrospect from performing automated backups. Dantz has fixed this problem in Retrospect 4.0, but if you have this problem with SiteMill, you should ask Adobe to fix it.

FrameMaker
When the Substitute System Font feature is enabled, FrameMaker may refuse to launch, claiming it “cannot initialize the font arrays”. This problem is a bug in FrameMaker, and I have received several reports that Adobe has fixed it in the latest version of FrameMaker. If you do have this problem, try turning off font substitution in Kaleidoscope, launching FrameMaker, and then turning font substitution back on. This bypasses FrameMaker's font checking, and it may prevent the problem when you launch FrameMaker again.

WindowShade
Kaleidoscope now collapses windows when you double click the title bar, so there is no longer a need for Apple's WindowShade control panel. Kaleidoscope works just fine if you leave WindowShade installed. However, when you double click a title bar, the window collapses in two stages and you may hear two sounds. If this bothers you, just disable WindowShade.

Stickies
Windows in Stickies do not have a WindowShade widget. This is because they do not need one! To collapse a Stickies window, just <option>-click on its zoom box. This is a feature of Stickies, not of Kaleidoscope.

Finder Window Background Color
When you quit from an application that modifies the system color palette, some Finder windows may be left with splotches of random colors in them. This will go away as soon as the offending windows are re-drawn. This annoyance is inherent to the system, and nothing can be done about it. This problem happens only in 256 colors.

Now Menus
If you are using Now Menus, it overrides the Kaleidoscope system font settings in some menus. If you want all your menus to use the system font you have selected in Kaleidoscope, set the font in Now Menus to “Default” and set the size in Now Menus to the same size you are using with Kaleidoscope. There really is no problem here, but some people are not aware that Now Menus provides font and size settings and may think this is a bug in Kaleidoscope.

Director, SoundEdit, FreeHand, Fontographer, form•Z RenderZone, InfiniD, DenebaCAD
The menus in these applications are black and white instead of using Kaleidoscope's menu colors. These applications are excluded intentionally because their custom menu routines do not support color correctly.

Eudora
With some system fonts, the icons at the top of Eudora message windows overlap their check marks. The fonts that come with Kaleidoscope have been specially modified to avoid this sort of problem. In particular, if you want to make Espy Sans your system font, you should instead use the Espi Sans font included with Kaleidoscope.

ClarisWorks
With some system fonts, the keyboard shortcuts in ClarisWorks menus get cut off. The fonts that come with Kaleidoscope have been specially modified to avoid this sort of problem. In particular, if you want to make Espy Sans your system font, you should instead use the Espi Sans font included with Kaleidoscope.

PopUpFolder
The pop-up menus drawn by PopUpFolder do not use Kaleidoscope's menu colors. PopUpFolder's custom menu routines do not support color menus, and there is nothing I can do about this.

BeBox: Command-Clicking Finder Window Titles
Command-clicking on the title of a Finder window normally pops up a menu of all the window's parents, so you can quickly move up the folder hierarchy. Unfortunately, the Finder expects window titles to be in the middle, not at the left where BeBox puts its tab, so command-clicking on the tab does not work. There is nothing I can do about this, I'm afraid. However, you can still get the popup menu if you click in the middle where the Finder expects to find the title; BeBox gives you a six pixel thick border at the top of the window, so there is still room to click.

BeBox: Panorama, First Class, Lotus Notes
These applications all assume that the window title bar extends the full length of the window, which is no longer the case with the window tabs in the BeBox color scheme. Panorama normally gives you a popup menu if you click the window title, but it assumes that the window title is in the middle, not at the left where BeBox puts its tab. As a result, that popup menu is inaccessible. The First Class client attempts to put a progress bar in the window title bar, but with the shortened window tabs, this progress bar spills over onto the desktop (or whatever is behind the window). Lotus Notes has a similar problem.  I am working on a way to exclude these applications from the window patch when the BeBox color scheme is selected.