There is a 30 second publish timeout in InfoPath with Browser based forms. My understanding from the InfoPath team at Microsoft is that you can't workaround this issue in MOSS 2007 (it's not an issue in SharePoint 2010).
Are you getting this error message after about 30 seconds or well before?
If you think this is the 30 second timeout issue you need to look at the logic in your form and see what you can do to limit that to try to get the publish time down. The more logic in your form the longer it takes to publish.
Ted