Glad to hear you are liking it!!
That sounds like a bug, let me try to investigate what might be happening..
Having said that, I have a much easier workflow for you if you are doing this often:
Go to the Modify Format dialog as you are doing, and SAVE your settings as a preset, and give it a nice name, like "Remove Blanks".
Ok now copy your clip to the clipboard, and go to where you want to paste it, and hit Ctrl+Alt+Q to bring up quick paste menu,
then hit T for "Formatting Presets" submenu, and choose your saved preset "Remove Blanks", and it should do the action and then paste it in your target app.
1. This won't change the clip in CHS
2. This can also be used to change text in place -- so you can go to your text editor, select some text, and then do Ctrl+Alt+Q and select the transformation and it will first copy the clip, then transform it, then paste it over original. This is the fastest way to change text in place.