Look at the C:\JTS\log.txt file and see if you got any errors reading, writing to or saving one of the *.lyt files.
Yes this has been happening to me recently as well. Sometimes a page will disappear, and the stocks on that page will be added to a different page I have set up. Also, sometimes I will try to change the name of a page, and I will get a message that the page already exists, when there is no page with that name. Frustrating!
I should also mention that it looks as if the TWS damage was done during the TWS shutdown or very shortly thereafter. My TWS layout was fine on Thursday, I did a backup after shutting everything down that evening, but a restore from that backup didn't bring back my missing TWS pages. I had to go back to Wednesday night's backup to get everything back the way I expected.
I restored these directories: C:\Jts C:\IBJts C:\Program Files\Java C:\Program Files\Java Web Start just to be sure I covered everything. It's likely that some of this was unnecessary. Perhaps someone can tell us what the minimum is.
If you are using stand-alone TWS, then folder: C:\Jts\dciijtglt needs to be saved as back-up. That's what I do once every few days. recently, when I lost my tws pages, I was able to recover by copying the folder back. If you are using web version of TWS, then C:\IBJts\dciijtglt is the folder. IB folks: if you are reading this thread, food for thought: Why not provide an option for automatic back-up Or provide tool link in TWS for back-up feature? I understand, Fidelity provides link in their ActiveTrader window for back-ups. Thanks.