Hej Bence!
I only just saw your reply, so I opened iolite to look at the file to be certain I was about to send you the correct one. However, the program greeted me with an upgrade notification, so I did. After the upgrade when I opened the file and looked at the images, it is now showing positive numbers for Mn. I have done a new export of the images and metadata, and, sure enough, the matrix is also showing positive numbers.
Therefore I guess that it somehow fixed itself in response to something that changed in the upgrade, so thank you. If you still want the iolite file anyway, or if you want me to send the old matrix csv file with negative numbers to compare with the new one with positive ones, I can send them, but given that the problem went away, I suspect that they won't be of much use.
Cheers,
--Riia