DFSR is not replicating SOME replication folders

I have two file servers, which we'll call fs-01 and fs-02. They have one replication group, which we'll call RG-01. Within that replication group are 25 sets of replicated folders. Its clear (by manually looking) that replication is not occurring in 3 of those 25 folder sets. Heres a dump of my troubleshooting so far

1. The servers are virtual running Windows 2008 R2 in a ESX5.1 environment. Underlying storage is iSCSI SAN. The servers are at 2 different locations (HQ and Hotsite) connected by a 1GB P2P network. The network is trunked across the P2P, though fs-02 is on a different subnet and is defined as such in sites and services.
2. I inherited this system about 5 days ago. Two weeks prior to that, a network architecture change (the trunking) caused some instabilities in the underlying SAN storage system. By all accounts those have been resolved now.
3. When I run the "Create Diagnostic Report" and create a propogation test and subsequent report the test files at 22 of the 25 folders are replicated nearly instantaneously (< 1 sec)
4. I ran the same propogation test in the three affected folders, and 3 days later they still show as "Incomplete tests" - which I take to mean they havent replicated.
5. If I run a dfsrdiag backlog /Rmem:FS-02 /Smem:FS-01 /RGName:RG-01 /RFName:"Folder name" from the command prompt it returns "No Backlog - member FS-02 is in sync with partner FS-01. Operation Succeeded. It even says this despite the fact that diagnostic test files still show as not yet synced in the report.
6. These replicated folders are GIGANTIC - 3.4 TB, 8 TB, and 1 TB with individual file sizes sometimes as large as 80 GB, but with (relatively speaking) few files in each individual subfolder - . The staging quote for these 3 volumes is set at 750 GB. All the other replicated folders have a staging quote of 10 GB.
7. I am ASSUMING that the files in FS-02 were in fact replicated, and not seeded, and that replication worked once upon a time for these folders. That said, I DO notice that these 3 folders all have special characters - ( and ) to be precise - in them.
8. There are no errors in the application or system logs on either server for DFS-Svc, DFS Replication, DFSR, or DFSR Audit. There are a handful of info notices for routine things like "DFS Server has finished initializing"

Anyone have any thoughts, or additional diagnostic tests I can run?