Added Firefox 45.8 to Environment as described in JENKINS-42626.
I believe this is the issue of the browser and I'll test with various browsers whether it reproduces. At least, I couldn't reproduce it with Firefox52.
(I'm not sure I can install an older version of Firefox)

Could not reproduce in my environment.
"By combination filter" works perfect with any browsers as far as I tested.
Please report more detailed steps to reproduce the issue.

Tested with Windows 10, jdk1.8.0_92.

Steps to test:

1. Install Jenkins 2.55.
2. Complete the setup wizard.
   • Install no plugins.
   • Continue as admin.
3. Install matrix-combinations-parameter-plugin 1.1.1 in Manage Jenkins > Manage Plugins.
4. Create a multi-configuration project "test"
   • Add axis: User-defined Axis
     • Name: axis1
     • Values: value1 value2 value3
   • This project is parameterized
     • Add Parameter: Matrix Combinations Parameter
       • Name: COMBINATION
       • Add shortcut link: By combination filter
         • Name: combination1
         • Combination filter: axis1 in ["value2", "value3"]
       • Add shortcut link: By combination filter
         • Name: combination2
         • Combination filter: axis1 in ["value1", "value3"]
5. Go to "Build with Parameters"
6. Test combination1, combination2

Results:

• combination1

  Browser	value1	value2	value3
  Firefox 53		x	x
  Firefox 45.8.0		x	x
  Firefox 45.9.0		x	x
  IE 11		x	x
  Chrome 58		x	x
  Edge 38		x	x

• combination2

  Browser	value1	value2	value3
  Firefox 53	x		x
  Firefox 45.8.0	x		x
  Firefox 45.9.0	x		x
  IE 11	x		x
  Chrome 58	x		x
  Edge 38	x		x

Reopen the ticket when you report the detailed steps to reproduce.

Hi,

I tested with your values and indeed it worked.

The minimal project I was able to reproduce the issue on is using a yaml axis for both axis.

I used this in the yaml file:

axis1:
  - value1
  - value2
  - value3

axis2:
  - column1
  - column2
  - column3

And in the project I declare 2 yaml axis from the file, axis1 and axis2 and two combination filters combination1 and combination2, with «axis1 in ["value1" "value3"]» and «axis2 in ["value2" "column2"]» in them.

None of them works, they uncheck everything.

This is an issue of Yaml Axis plugin.
Changed component/s and assignee.

Matrix-combinations doesn't work expected because `Combination#toIndex()` doesn't work for yaml-axis, that because `YamlAxis#indexOf` doesn't work.

The implementation of `Axis` assumes that axis values are set to `Axis#value` but `YamlAxis` doesn't as its values are computed dynamically.
`YamlAxis` have to override all methods of `Axis` that uses `values`:

• indexOf
• hashCode
• equals

I believe `Axis` is badly designed (it assumes values are static), but it's difficult to redesign to preserve compatibility.

`hashCode` and `equals` might not need to be overridden as the yaml file name is stored to `values`.