I am no expert on the Amiga version of the Newtek Video Toaster, having put only a couple hours into using one, and not very focused hours at that. Compared to the later Windows versions, there are a bunch of caveats I was not prepared for, which are not intuitive nor covered clearly in the manual.
You might be seeing references to a "Framestore" section that doesn't exist, an "Overlay bus" that doesn't exist, or "menus" that don't exist, among other things.
The different versions of the Toaster software are radically different. The 1.0/2.0 GUI are completely different from the 3.x GUI, and again from the 4.1, and again from the 4.2/4.3. You are reading a manual for the wrong version.
Sadly, not all versions of the manuals seem to be online. Your best bet may be to upgrade to a version that matches the manual you have.
On a real vision mixer, you can do whatever you want with the T-bar, including pulling it partway across, then reversing instead of finishing the transition. You can also usually perform the transition either by swinging the T-bar down if it's up, or up if it's down.
The Toaster T-bar only goes from top to bottom, and many of the transitions only run in one direction. If you have a simple fade, you can reverse it midway, but I don't think any of the graphical effects support this. The manual just says that "some" can only be run in one direction, but I think "most" might be more accurate.
You might find that when you perform a sphere or cube 3D effect, instead of wrapping the video around the cube as it flies offscreen, you just see a cutout in the shape of the object.
This happens when one of the framestores is occupied with a CG. You can identify this by the FREEZE button being highlighted. Click FREEZE to clear the DV, and now your effects will all work.
Symptom: Sometimes the color is just really badly out of whack, but not when you've just started up the toaster. It only happens after you've been doing stuff for a bit, or when you trigger 3D transitions, or when you take a freezeframe.
Cause: The Toaster has a digital framestore that can store a single fullscreen image. When doing ordinary switching it is not in use; the signal from the active camera is simply passed straight through to the output unmodified. If you're doing a CG overlay, the CG lives in the framestore and the card switches to it only for the pixels where the overlay will appear.
The Toaster's digitizer can get miscalibrated, so when you put an image into the framestore, the hue is off. The reason you only see this sometimes is because the inputs are only routed through the framestore if you request it, or if an effect needs that, or if you take a freezeframe.
You can detect if the image is being routed through the framestore, because three buttons will be simultaneously selected on the same bus: An input, and both DV1 and DV2 will all be yellow. Click the input again, or click another input and then back, and DV1/2 will clear. If your color returns to normal, this is your problem.
Solution: Run the Autohue tool, inside the Toaster folder (possibly under Utilities.) It will usually tell you how you need to connect the inputs and outputs on the card; follow the instructions precisely and it will fix your problem.