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The KEEP SELECTED and the MERGE ONLY WITH SELECTION options will be turned OFF but elements will randomly merge. VERY frustrating. I use Illustrator instead of Photoshop for the purpose of keeping all the little strokes separate for easier manipulation, but half the time I find that the strokes are suddenly merged together even when I specifically keep that function turned off. Older versions of Illustrator never had this problem and I REALLY wish Adobe would fix this.
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Merge only with selection needs to be turned on if you don't want to merge.
Keeping it off means that everything will be merged.
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True. But it doesn't explain why things will randomly merge whether that option is selected or not. I'm not the only one with this issue. My colleagues have had things merge as well. The problem only started after we started using the latest version of Illustrator.
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Did you reset the preferences when updating?
Did you already reboot the computer?