Not sure if anyone has had this issue.
Really, the timeout for PHP should probably be increased - but this will depend on the load placed on the OAv2 server.
I have found when (ok, admittedly overloading) auditing 20 machines from my desktop - which is also the OAv2 server (Core2Duo, 4GB), another 20 from a second machine and another 20 from a third machine, several audits ( ~40) did not complete (out of the ~10,000 audits that were run). I could tell because after all audits were completed, there were rows in sys_man_audits that had values in the audit_debug column. This column should be set to blank when an audit is completed.
Attached is a report you can use to check your own installs to see if you have any system's that did not complete correctly.
I solved this by running this report, extracting the PC names (using the Excel report), editing all the systems on the report and setting their "status" variable to deleted. I then used the "audit_list.vbs" with the PC names that I extracted, re-ran the audits for those systems and all was well. I also manually set the sys_man_audits.audit_debug column to blank upon completion of all audits. Painful
I have a couple of thoughts as to how to overcome this.
In the meantime, I would ask that you use the attached report to check your database for incompleted audits.
If you find ANY, please don't hesitate to post in this thread. I have no idea of how severe this issue is, nor how many people this is affecting.
Apologies for the bad code and thanks in advance for reporting any occurances.