I'm not sure what problem you are having with netflow on your bundle interfaces. You may wish to open a TAC Service Request to troubleshoot it.
Regarding how it works...
Netflow for IPv4 on the CRS-1 for bundle interfaces has been supported since IOS-XR 3.3.
You configure the flow monitor on the bundle-ether interface and not on the individual bundle members.
There is a Netflow management agent (MA) process running on the RP as well as each linecard.
The MA on the RP is responsible for all the configuration of global interfaces like bundles.
The MA communicates with the Execution Agent (EA) process that runs on the linecards where interfaces that have Netflow configured are located. The EA participate in the verification on of the configuration and the programming of the hardware (egress and ingress PSE) to enable the feature on the interfaces. The netflow microcode on the ingress and egress PSEs of the linecard is programmed with the the information regarding on what interfaces Netflow is enabled and the sample rate. Then the sampled packets go through the microcode where fields of interest are extracted and a flow record packet is created and punted to the Netflow server process on the LC where the flow monitor cache is populated. The Netflow Server creates the cache and updates it with the records from the hardware. Then it ages the entries from the cache and exports the packets to the Netflow collector.
