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Custom Property Fields on Macs

We are a big ePO shop, and we had been using the Custom Property fields as a particularly efficient way of asset management and organization within ePO. In a nutshell, we were assigning a serial number to Custom Prop 1 when the Mac was first provisioned, and then periodically sending back a status update (for another application) along with a timestamp for Custom Prop 2. We were using ePO 4.6.5 with Agent Management Extension 4.6.

This past week, we upgraded to ePO 4.6.6 and Agent Management Extension 4.8, and now our custom property fields are being lost. That is, only the value that is set most recently is stored in ePO, all other values are blanked out. To clarify,

1) Run msaconfig -CustomProps1 "test 1"

2) Sync using cmdagent -P

3) "test 1" is in ePO custom property 1

4) Run msaconfig -CustomProps2 "test 2"

5) Sync using cmdagent -P

6) "test 2" is in ePO custom property 2, custom property 1 is now blank

We did not have this issue prior to the upgrades, and I don't see anything in any kind of release notes or KB articles about it. Also, before, it seemed like this was the logic of msaconfig:

1) Run msaconfig

2) It creates the CustomProps.xml in scratch

3) Sync, and CustomProps.xml is removed

Now, the CustomProps.xml seems to be persistent, as it remains after a synch as well. Has anyone else seen this? Is there anyway to allow for individual custom properties to be set without over-writing the existing values for the custom properties you're not editing?