Which version of the plugin and jenkins server did you upgrade from?

The updated Jenkins version probably was 1.569; the JaCoCo plugin version was the version preceding 1.0.16.

I have the same problem. Jenkins 1.578, JaCoCo 1.0.15.

When I'm in the default view, the bug does not occur. When I'm in a specific view, The URL has the same structure as the OP:
http://URL/jenkins/view/MyViewName/view/MyViewName/job/MyJobName/lastSuccessfulBuild/jacoco/ .

The "view/MyViewName/" is repeated twice, which causes the link to fail.
Removing one or both of the occurences works just fine; the report is generated ok. The problem concerns the link only.

It seems to happen only for views other than the default view, seems Jenkins provides an different ${job.url} then, not sure how to fix this, will need to dig a bit more into it.

Seems to be a general problem in Jenkins, I have reported JENKINS-25113 to track this, there may be a workaround possible that I will try to put in place.

Code changed in jenkins
User: Dominik Stadler
Path:
src/main/resources/hudson/plugins/jacococoveragecolumn/JaCoCoColumn/column.jelly
http://jenkins-ci.org/commit/jacoco-plugin/44b5d298f3b36f57bc420d333b9ba56bbbac4850
Log:
JENKINS-23623: Fix URL in JaCoCo Coverage Column in non-default views, works around JENKINS-25113

Applied workaround via https://github.com/jenkinsci/jacoco-plugin/commit/44b5d298f3b36f57bc420d333b9ba56bbbac4850, will be contained in next release 1.17