In case that test page is changed, here is the process I followed:

See this page in the users guide: Personal Synonyms

Chromosome synonyms
Here is an example chromosome synonyms file: chromosome.txt

KlingonChr1 Chr1
KlingonChr2 Chr2
KlingonChr3 Chr3
KlingonChr4 Chr4
KlingonChr5 Chr5

Here is an example bed file, made by taking segments from the A_thaliana_Jun_2009 gene annotations and replacing the chromosome names: KlingonGenes.bed

NovelChrom 3630 5899 AT1G01010.1 0 + 3759 5630 0 6 283,281,120,390,153,461, 0,365,855,1075,1543,1808,
KlingonChr1 5927 8737 AT1G01020.1 0 - 6914 8666 0 10 336,633,76,67,86,74,46,90,48,167, 0,509,1229,1456,1636,1834,2014,2308,2489,2643,
KlingonChr1 6789 8737 AT1G01020.2 0 - 7314 8666 0 8 280,294,86,74,46,90,48,167, 0,367,774,972,1152,1446,1627,1781,
KlingonChr1 11648 13714 AT1G01030.1 0 - 11863 12940 0 2 1525,380, 0,1686,
KlingonChr1 23145 31227 AT1G01040.1 0 + 23518 31079 0 20

etc.

Notice that there is one entry for a chromosome (NovelChrom) that is not in the synonyms file.

As per the directions in Personal Synonyms, add this chromosome.txt file as a chromosome synonyms file. Restart IGB.

Start IGB and choose the A_thaliana_Jun_2009 genome. Load the exBed.bed file. Use the "genome" load mode, the file only includes a scattering of annotations.

If IGB creates new chromosomes labeled "KlingonChr1" etc, indicating that the link between chromosome "KlingonChr5" and "Chr5" is not functioning.

I noticed that in 9.0.0 (where the chromosome synonyms seem to be working fine) there was no window prompting me to restart IGB. However in v9.0.1, there was. So I looked for issues that have dealt with synonyms.
This issue might be related: IGBF-1187

In fact, it looks like the comments from that issue deal very directly with this problem.
It looks like I made a branch with a fix that was not never merged. The comments leave off where I assign the branch to someone else for testing.
And now the issue is unassigned.

Please add link to your branch that deals very directly with this problem.

This is the branch that deals with IGBF-1187
https://bitbucket.org/IvoryBlak/integrated-genome-browser/branch/IGBF-1187-b

This wasn't all that long ago, but I have no memory of it.
I need to rebase it and test it to see if that actually solves this issue.

I rebased that branch and I tested it on my local machine (mac).
This seems to be working fine. --> ready for first level review.

The branch you should test is here: https://bitbucket.org/IvoryBlak/integrated-genome-browser/branch/IGBF-1187-b
The instructions for adding a chromosome synonyms file are here: https://wiki.transvar.org/display/igbman/Personal+Synonyms
The release testing instructions are here: https://wiki.transvar.org/display/ITD/Synonyms
--->in particular, see the "good" and "bad" images and the test files.

That gives you the general instructions.
Here are the instructions specific to this fix:

Go to the A. thaliana genome, and load the KlingonGenes.bed file. The list of chromosomes should look like the "bad" image.
Now add the chromosomes synonyms files. You should be prompted to restart IGB. Restart IGB.
Go to the A. thaliana genome, and load the KlingonGenes.bed file. Now the list of chromosomes should look like the "good" image.

clear preferences.
Go to the A. thaliana genome, and load the KlingonGenes.bed file. The list of chromosomes should look like the "bad" image.
Return to the home screen (click "species" above the genome pulldown).
Now add the chromosomes synonyms files. You will NOT be prompted to restart IGB. Do NOT restart IGB.
Go to the A. thaliana genome, and load the KlingonGenes.bed file. Now the list of chromosomes should look like the "good" image.

Restart IGB (do not clear preferences).
Go to the A. thaliana genome, and load the KlingonGenes.bed file. Now the list of chromosomes should look like the "good" image.

Followed the above steps and tested. It works fine on windows.

I created a pull request.
Branch name is IGBF-1187-b

Merged to master.