System Restore itself doesn't get infected rather a restore point in the system volume information folder in XP contains the virus deleted from a system folder, it is a simple repository for data.
I don't believe System Restore brings things back automatically, otherwise everything would be restored. Something has to retrieve it and restore it, either a user initiated selection of a restore point or something that knows what location of which restore point that infected file. So that something has to be running and should be able to be found by something like HJT.
For me that can really only be System Restore as the restore point names are generated by SR, so how could a piece of third party software know which restore point contains the virus so it can be retrieved.
My belief is the virus is getting back in the same way it arrivrd previously (so the exploits, etc. have to be closed), because it is the same virus it is likely it will have the same name and will be stored in the same location. So yes it comes back but I don't believe it is because of system restore, but yes disabling system restore will clear old restore points so it can't be manually restored.