Hi Gnanendra, I have not worked directly into Carrier -Aggregation but have some thoughts which I can share.
1. RRC Connection Reconfiguration message which is sent from eNodeB to UE, carries secondary cell information.
2. RRC Connection reconfiguration complete message is an indication that tells UE has accepted the configuration.
3. For the carrier aggregation, PUCCH format1b (extended version) and PUCCH format 3 are used. If you have doubt whether UE has setup for CA or not, please check the PUCCH format for HARQ ACK/NACK. PUCCH format 1b is used when UE is using 2 carriers while PUCCH format 3 is used when more than 1 secondary cells are being used for carrier aggregation.
This is my view to find out the solution of your problem.
I expect If someone has working experience on this feature can provide better answer.