Consider the following following example.

If I mark and copy the equation:

Then paste it again after the first equation, the expected behaviour is the following:

But with indentation mode "Indent ant Unindent Automatically" everything except the first level of indentation is lost:

And with indentation mode "Keep indentation" an extra tab character is added to the pasted equation:

With indentation mode "Ignore indentation" I get the expected behaviour, but it is a pain to work in this mode since any time I press enter to get a new line the indentation is ignored (as advertised).
I suggest modyfying the mode "Keep indentation" such that no extra tab is added. Another way is to make a new indentation mode that keeps the best qualities of "Ignore indentation" and "Keep indentation".
Anonymous