This is duplicatable. Create an Action by opening the Guides DB and specifying the margins to be a percentage. When trying to run the action on other images the percentages are lost and replaced by a measurement. This was an issue that was fixed about a year ago, but now it's back.
Can confirm. I created a new guide layout which adds a 5% margin and then saved that as a preset. After creating a new canvas which is a different size, the preset is loaded as the pixel amount from the original canvas. In my case, this was 141.75px. Found another bug along the way, too. If you create a new artboard, the menu item New Guide from Shape becomes active, but if you select it, a warning pops up that the command is not available. I'll log both of these. Thanks Martin.