Never encounterd this... maybe something corrupted in the system data file?
You may try the following:
1. Go to the game folder, there should be a "save" subfolder. If not, then try to find either "C:\Users\(UserName)\Documents\Purplesoftware\クロノクロック\save" or "C:\Users\(UserName)\AppData\Roaming\Purplesoftware\クロノクロック\save" (depends on where you've chosen to place the save folder during the game's installation).
2. Rename the "system.dat" file to something else.
3. There should be a backup of the abovementioned file (called "system.bak"). Rename that file to "system.dat".
4. Run the game and see if the backup works. If not, then you may have to rename that too to reset the states back to the beginning (or apply a 100% save at the reply no.2 above).