Fixed in r3409.
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The r3409 is fine. However it creates version names, that contain the name of project you were creating the version in. This is fine in normal shared versions, however "system" versions are not tiet to particular project. So the project you were in, should NOT be displayed. And there is no way to create system version that is not tied to project.

The solution is in my opinion simple. system versions should not display project at all, just display "Global - <version_name>". I suggested this fix in #4728 as well.

Just remember - system versions are meant for whole redmine installation, so should not bear the project name, which is misleading.

Patch for @format_version_name(version)@ attached.

For r3409 the patch will be changing line 215 in source:trunk/app/models/query.rb@3409#L215 like this:

<pre>
- @available_filters["fixed_version_id"] = { :type => :list_optional, :order => 7, :values => system_shared_versions.sort.collect{|s| ["#{s.project.name} - #{s.name}", s.id.to_s] } }
+ @available_filters["fixed_version_id"] = { :type => :list_optional, :order => 7, :values => system_shared_versions.sort.collect{|s| ["Global - #{s.name}", s.id.to_s] } }
</pre>

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> This is fine in normal shared versions, however "system" versions are not tiet to particular project.

System shared versions *are* tied to a project and you can share system versions from different projects.
So having the project name makes sense.

For your need, you can name your project with your system versions "Global" as a workaround.
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duplicates,Closed,4559,Add a version filter to the global issues view