We have seen the GroupWise API behave ‘strangely’ when processing a larger folder (4,960 or more messages). We recommend to split the larger folder to smaller folders. In your case, you may consider to create a find results folder with less then 4960 messages. Alternatively, you may try to save messages by smaller brunch from the large find results.
Hope this helps. If you have any further questions, please do not hesitate to contact us.