First off, you're already scaling in Truespace the way you should be. You have to actually use a calculator if you want to keep proportionality, and it does use multiple type-ins, so it's got it's drawbacks. But it's the closest you're going to find to a uniform scale in Truespace, and it's really not that bad once you're used to it. You usually only use it once on a given model, so it would take less time than opening a different program to do it. Secondly, there is no reason that 3dex should be messing Truespace up, but it's rare that a 3rd party tool works exactly correct on a proprietary format anyway. The reason object rotate may matter is that it's sweeping the transform through the desired rotation, rather than simply applying a transform to the model all at once, so it concievably could be running out of allocated memory on a moderately complex model (by Freespace standards). If you aren't already, use the object properties (again) to set the orientation; any half-decently designed model will be set facing down one of the three axis and so some combination of 0, 90, 180, -90 for rotation in x, y, and z should make it face the way you want it to. The other option is to not use 3dexploration at all, which may in truth be the way to go. Texture replacement can be done easily in truespace (the paint roller tool) or at the POF level, so there's no reason to go to a third program to make it work. No modeling experience required.
