Hi Geetika,
If I understood your issue exactly initially your able to see default business system value in "From Business System" filter in "Browse Product Category Tree View" but now your not able to see.
I have tried to replicate your scenario with integration tab hidden and without hidden. But I was not able to replicate the issue which you have stated, I checked in Application Version: 9.0.06.01 and 9.0.17.00.
Browse Product Category Tree View is Java execution based query in that From Business System filter type is object reference. This filter have Prefill value from cache.
Please let us know the version which your using.
Regards,
Lava.