Can you please provide more details about the problem and about your instance? For example:
Which Fisheye version is being used?
Has this problem always happened, or has it started happening recently? If the later, what were the most recent configuration changes that took place?
Does the problem happen when you search code from any repository or just from specific repositories?
Do you see any errors in the application logs when the problem is replicated?
When the problem happens, do you notice any CPU or memory usage spikes in the server hosting Fisheye?
How long do you need to wait until you're able to see line counts?
Which URL is presented in the web browser when you replicate the issue? This will help us reaching a similar URL in local instances and trying to replicate the issue.
Regards,
Felipe
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