What version of VP is being used? Suggest that 8.32 be installed, where the behavior you describe isn't evident. For licensed users upgrades are free for up to six months from purchase date. After that, VP will continue to fully function but a fee will be required in order to register the newest. Retain your old install file and registration info.
Using that version, loaded a 9:16 that was sideways into the bin, right-clicked and rotated it, then placed it on the sequence. There was no cropping.
It's unclear what you mean by "now cropped to the width of the original - the sides are missing." If a 9:16 clip is rotated to the correct position its aspect ratio should not change.
Please upload the clip in question to a free server, make it public (share it), copy the shared link and post it here. Someone will check it out.