Needs to be checked whether there is a race condition.

I think you should also be able to change your startup application command of 
Diodon to
G_MESSAGES_DEBUG=all diodon > diodon_debug.txt

you will have to give the txt file a full path e.g.
/home/username/diodon_debug.txt

Haven't tried this before but should technically work... maybe this way
you are able to reproduce the issue and with a debug log file.

I will have a closer look at the source code to see whether I find
anything which could cause this.

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https://bugs.launchpad.net/bugs/1383013

Title:
  Diodon on 14.10 does not clear history consistently

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