Hi,
Sounds to me like some bug.
There is no difference to my knowledge with the ACL format regarding simple "remark" ACL lines so I can't really see a reason why they wouldnt be entered in their original form to the ASA configuration.
But it's hard for me to say certain about this as I have not used the ASA itself to migrate configuration during boot. I have done them manually.
Actually, while I was typing this message I found this bug. Its probably the one you have run into
Copy/Paste the whole URL or click the BugID part of it.
https://tools.cisco.com/bugsearch/bug/CSCto87589
Hope this helps
- Jouni