Retested with a video file - positioned, scaled, cropped and then saved and reloaded, but couldn't duplicate the problem in v11.97.
After reloading the project click the CROP header to see if the effect has held... 
Try this. Go to OPTIONS | MEDIA tab and in the Advanced section at the bottom, click on Default and choose None (CPU only).
Restart VP. Under OPTIONS | DISK tab Clear Unused Cache Files. Restart again.
If no joy, please share the project, or a portion that demonstrates the issue. The process is easy, quick and can be done privately. Just follow these steps...
Back up --- With your project on the timeline, click on MENU at the top-left. Click FILE|BACK UP PROJECT FILES TO FOLDER. Choose a folder and SELECT FOLDER.
Upload --- Use a free server - Google Drive, MS OneDrive, etc.* - to upload the saved, numbered FOLDER. Do NOT upload the individual VPJ or export file.
Get link --- Get a public link. If using Google Drive click GET SHAREABLE LINK. If necessary change "restricted" to "anyone with the link can view"
Share --- Click COPY LINK | DONE. Paste that link here, or click the folder at the top-right of this forum to message it privately to me. It won't be shared.
* Before uploading, right-click the folder, click PROPERTIES. Look at the File Size to confirm that it's not too big for the free space on the server.
Then it can be seen just as you see it, for analysis.