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Ok, I was experimenting for about 30 minutes, and found the fix for my case.
I replaced your 512-514 lines (of CF7DBPlugin.php)

if (ob_get_contents()) {
  ob_clean(); // Fix bug where download files can be corrupted
}

with next lines

while (ob_get_level()) {
  ob_end_clean();
}

Notice, I had to remove if (ob_get_contents()) statement, because with it the file remained corrupted.

I still have the problem with downloading of corrupted files. Tried only with .doc files, but I think the same will be with onthers. If I open downloaded from CFDB file in Word, it is corrupted. I thried then to open downloaded file with Notepad++ and save it as UTF-8 without BOM. After this the file was opened fine with Word.
I tried to modify ajaxFile() like you tell, but this didn`t work for me.
Can you tell me where I should place the fixing string? And what exactly its` content?

UPDATE

May be CFDB is corrupting files when saves it into db?

How about adding qTranslate support in your plugin? I mean custom fields text in your plugin, like: “[:en]Name[:ru]Имя”

Sad, but this plugin is unusable still.
I made russian localization for it, but author still can not move files from “ru_RU” directory to “lang” so it will work. And this is only one of 100 bugs in this plugin.
It is sad, because all similar plugins are not free (PRO-verisons, free ones are useless)