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we don't have citrix accelerator boxes in use, but as I would assume, especially with IDS mode, there should be no blocking, at least none without alerting.
We have a Riverbed accelerator in use though and never had any issues with our McAfee's in inline IPS mode.
To investigate the issue you could do some packet capture at a firewall, if in place before or behind the IPS.
Hope you can solve the issue!
Do you think that back to back IPS could cause a problem ?
Sorry, but I don't have a clue. Never tested it.