I'm a little lost by your question. I just tested this, checked the data in the database, and tested a view. The "other" option's value is stored with the other checkbox values and is always displayed as the final selected option in a view if there is a value for the other option. Formidable does not save empty values.
From what you expressed in your post, there is one clue missing in your example for which I made an assumption. In the checkbox you have four letter choices plus other. In your expected response, you have 3 letters plus the value of other. My assumption is that "all that apply" means A B C plus other.
This is the problem I ran and received the results as you expect them. I have a 3-value checkbox on my play form where the 3rd option is other. The first 2 options are the defaults for new fields. This is the data from that field when stored in the database:
a:3:{i:0;s:8:"Option 1";i:1;s:8:"Option 2";s:7:"other_2";s:12:"test-option3";}
If you're not familiar with this data format, it is a PHP serialized array. This says I checked three options and the value of my other option is test-option3. This is accurate. Take note "other_2" is an internal pointer used by Formidable to make the magic happen.
This is displayed in the view:
Option 1, Option 2, test-option3
I hope this helps a bit. If this explanation doesn't help solve the problem, make sure Formidable and all add-ons are up to date, and you are on a current version of PHP. And depending on how long you've been operating this system, the issue may be database maintenance required as well. Formidable has been around for a long time and a lot of transitions have taken place over the years in terms of database efficiencies. I'm seeing a lot more clients that are bumping up against "illegal mix of collation" errors because of the evolution of unicode.
If all else fails, open a ticket with Strategy 11 if your license is current. Check back if you need a developer to help you, but be aware, this will be an expensive repair if it's your system and Strategy 11 or your host can't help. Good luck.