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Thanks for the replies and commits already made. So, our situation is that we have pretty busy production Jenkins system, so there's only limited experimentation can be done there, and in limited time I had to look into this issue, I traced it just to the source line in the original description above. This is also 1st time I looked into SCM polling, so I don't know how related data is stored and other details.
But job we had issues to is actually public: https://ci.linaro.org/job/trigger-linux-ltsi/ . As you can see (note: builds in question may expire in a week or two), from build #132 Feb 23, 2015 11:33:10 AM to build #161 Feb 23, 2015 1:58:09 PM , build triggered every 5 mins, which is SCM polling period for that job. But typical poll log looks like: https://ci.linaro.org/job/trigger-linux-ltsi/160/pollingLog/ (content quoted above in the original description).
Kanstantsin: The repo is public, running git command from poll log, I get the expected output (I also thought that maybe there's stray space or something gets parsed, but I confirmed it all looks ok). Will try to look up those build.xml's as a next step.