Dear Nagaraj,
we faced exactly the same issue and we tried to solve it following the proposed solotion but unfortunately did not work.
After "Reinitialize" the service regestry nothing changed and we still have the same error message (SRT Framework exception: Error: Register application failed: Application Error: Logical Key 'xxx.SystemName.xxx.SystemNumber.xxxxx.SystemH' already registered with Application Key 'xxxxxxxxxxx') when we try to save a web-service configuration in our system using soamanager.
We are currently using SRM 7.03.
Any other suggestion?
Thanks in advance
KR
Fabrizio