I've seen this before but I'm not 100% there is ever a single cause for this. Before you do anything else you need to be completely sure that your snapmirror setup across both sites is valid and i mean valid according to the install and admin guide that ships with the SRA and also with this guide http://media.netapp.com/documents/tr-4064.pdf
There are many ways to configure snapmirror, many options that SRA has for enumerating snapmirror, (ex ip_hostname_mapping), there are also different ways of defining connection names in snapmirror.conf and of course you then throw into the mix there are two sites so two sets of all of these configurations. You need to check your setup is consistent with the docs and also consistent at each site. Most NetApp "odd" issues I see relate to a mistake somewhere in the config or simply a setting missed (such as ip_hostname_mappings) that needs to be in place in order for things to work with the customers chosen naming conventions for example (long / short / fqdn or ip).
In the original NetApp 2.0 SRA there were some "Reprotect" bugs but those were fixed in later release. There was also an issue some customers hit where they turned on "autodelete" for the snapmirror volumes which caused reprotect to fail. This is mentioned in the SRA admin guide search for keyword "autodelete".
If you have time please go through your config. Are you using qtrees here as separate exports or simply the whole volume? In all of the above I'm assuming you've deployed a fairly simply snapmirror configuration. I have seen some odd multipath snapmirror setups with multiple destinations that have caused odd errors as well. Are you creating the snapmirror entries manually or via ops mgr?
I think you said you have logged an SR with VMware and IBM? did you log an SR with each company or is the initial call to IBM? Be useful to know the VMware ticket number.