Hi rovanuzo,
1) That is strange. We may need you to create a support ticket where you supply your configuration with us so we can test and try to replicate it with your files.
Please create a support ticket here:
https://support.holdemmanager.com/support/ticket/94
In the ticket please provide:
-A link to this thread
-Your hands exported from HM2
-Your NoteCaddy Definitions folder from here: C:\Users\[Windows username]\AppData\Roaming\HoldemManager\definitions
Please .zip the files and upload them to a cloud service like OneDrive, Dropbox, or WeTransfer.com and share the link(s) in the ticket.
2) I apologize for missing this. For this question I assume you are referring to HM3 and you have set your HUD to 'Arrange in Grid'. When using 'Arrange in Grid' the columns automatically widen to the longest cell in the column so that the grid maintains its alignment. You can uncheck 'Arrange in Grid' for your HUD in the HUD Profile Editor so that the badges are not able to move.
3) Thanks for the screenshot. I see what you're saying now. In the popups the notes are showing in the correct order that you've set, but the notes in the badges aren't. You have to add the notes in a certain order for a color definition (priority doesn't matter for the badge popups). If I remember right, the first note in a color definition will appear last. So for your example in your screenshot you would add them in the inverse order: 6-9, 9-12, 12-15, 15-18, 18-40 (assuming you want the larger stacks to show first). If this does not help, please share a screenshot of the color definition used for the badge in your screenshot.