Hi Sujit,
It could be due to hanged JCo Connections. Try below and see if it helps you.
1. Check and test all the JCO connections
2.Check the below notes too
581509 - Reasons for "timeout during allocate"
566566 - Timeout during allocate, syslog R49 CPICRC 027 SAPRC 456
3.Check the below link and set the gatway parameters
http://help.sap.com/saphelp_nw70/helpdata/EN/78/20244134a56532e10000000a1550b0/frameset.htm
set the gateway parameters:
gw/max_conn 2000
gw/max_sys 1200
4. Check the below Note
1522463 Hanging RFC connections to JCo RFC servers in AS JAVA
5.If above doesnt work, plan for latest SP Upgrade for ABAP and JAVA, which will surely resolve your issue.
Please do reach us if the above all doesnt help.
All the Best..
Best Regards
Kishore