Many thanks to all who have offered help and advice.  The following evidence 
strongly suggests a memory management problem to me:
1. I was able to perform "Check & Repair" on all accounts and subaccounts by 
dividing them up into smaller groups, saving, exiting and restarting GC in 
between.
2. If I tried to "Check & Repair" too much at once, GUI response would slow 
dramatically and GC would forget how to do things it had already done 
successful in the same session, e.g. saving, which, when attempted, produced 
messages like:
>>
* 22:08:34  WARN <gnc.gui> [gnc_builder_connect_full_func()] ggaff: could not 
find signal handler 'gnc_ui_file_access_response_cb'.
<<
I now have what I think is a working and fully checked file in GC 3.11 for 
Windows and will now try upgrading it to 4.8 in Ubuntu Studio.
My file does include Trading accounts, so Kalpesh's suspicions may be right.  
However, this raises the question of whether I need a newer version than 4.8 in 
Ubuntu Studio.

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