We have been unable to reproduce this issue with Formativ Runtime 126.96.36.199 and GroupWise 6.5.4. We installed Runtime and GroupWise in a clean Virtual Machine (with no applets), and set the threshold on the mailbox such so that it exceeded the size of the mailbox. The warning message would appear only once.
We tried various combinations of thresholds and limits in relation to the size of the mailbox, and also experimented with the attachment size settings. Again, we were unable to cause any warning message to appear twice.
To pursue this further, could you please send us the Formativ configuration information from a machine where the two warning messages appear. From the main GroupWise menu, select Help | About Formativ. When the about box appears, select the configuration tab, then press the copy to clipboard button. Finally, draft a new message to email@example.com and paste the content of the clipboard into the body of the message.
Could you also provide details of the mailbox size limitation settings in use, and the details of the messages that are appearing twice. I.e. is it the attachment warning dialog, message size warning dialog. Finally, any other information you feel may be appropriate would be much appreciated.