Version 12 is a joke, so I don't want to mention it. This problem existed since long long ago. You can do an experiment yourself.
1. Turn on unix regular expression option.
2. Input 4 lines of text and move cursor to the beginning of file. It may look like this:
|111111111
2222222222
3333333333
4444444444
3. In replace dialog input like this:
Fine What: ^
Replace With: #
And click Start. (This means I want to put a # in the beginning of a line.)
4. In Replace dialog, click Replace. (Suppose I want to replace one by one) You will find UE miss some lines so the result may be like this:
#1111111111
2222222222
#3333333333
4444444444
I have reported this problem to IDM before. I don't why they just don't want to fix it.

