JENKINS-4672 gives possibility to setup Marcurial debug flag.
When I switch it on, the all mercurial call is done with option "--debug".

The first command, during the build, checks if configuration of repository wasn't changed.
This check is done by comparision result of commad "hg showconfig paths.default" with jenkins configuration.

But there is a different output if the debug option is ON.
Without debug option :
$ hg showconfig paths.default
https://hg/hg/zpis

With debug option :
hg --debug showconfig paths.default
read config from: /etc/mercurial/hgrc
read config from: /data/hudson/.hgrc
none: https://hg/hg/zpis

So with the debug option, the mercurial configuration is always different as jenkins configuration.

Result is :
-----------
Building in workspace /data/hudson/jobs/vlk-pokus/workspace
[workspace] $ hg --debug showconfig paths.default
read config from: /etc/mercurial/hgrc
read config from: /data/hudson/.hgrc
none: https://hg/hg/zpis
which looks different than https://hg/hg/zpis
so falling back to fresh clone rather than incremental update

Workaround : Switch off the degug option.