The latest version of Crucible (3.0.2) is compatible with all versions of JIRA from 4.4 onwards. Please do not install such an old version of Crucible - 2.6 is unsupported and contains numerous bugs which have since been fixed.
It sounds like you're seeing that error because you need to enter the base URL for JIRA into fisheye withoiut the path. That is, something like:
Do not include the /secure/Dashboard.jspa
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