IIRC, emulator used to crash when you had an IR code in your config without a name such as 'Learned'.
Here's one way to isolate your issue. Create a new simple config with a button with a single delay on it. Emulate this config, if it works then this is likely your cause. You and figure out which button has the code causing the issue by using CCFTools to decompile your config to a CSF file plus bitmaps. You can open the CSF file with notepad or any other text editor of your choice. Search for "Learned" to determine what this looks like and then try searching for an empty string (be sure to include the double quotes "").
I also seem to recall something about MSXML6 but I think that was for the NG remotes.
