PokerTracker

On merge, my HUD appears in position on a few tables, and then on a few its out of place and all messed up. Any idea why? screen below:

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Without player names in the HUD it's hard to see what is wrong, but please read the Tutorial: Preferred Seating.

One thing to be aware of is that Merge do not specify the size of the table in their hand history files so if you join a 9-max table with 6 or less players and have the Adjust Qualifying Tables Limits option enabled then the table will be detected as 6-max and therefore the 6-max HUD will be used.
If you always play 9 or 10 seat tables then you can disable that option (Auto Import > Preferences, or you can use the PT-icon menu "Treat As" option to tell the HUD what table size layout to use.

I'm having trouble with this also. It seems as if PT3 assumes the default seat to not be at the bottom; if I were to change my seat in merge to the bottom and rearrange the HUD with respective stats near their owners, save the layout and apply it to all the tables, the HUD bounces the stats around in almost a triangular fashion: My stats that are correct on Table 1 in the bottom seat translate to my stats showing up on Table 2 in the upper left corner seat even though I am positioned at the bottom.

Please follow the above directions - the linked tutorial should help you get things sorted out.
If not, please report your problem so that we can check your config.

For clarification, would the bottom seat be Seat 5?

EDIT: I should probably learn to read the whole thing before I post, as I now found fancy diagrams :)

Not for Merge - on Merge it's seat 7. The linked tutorial has screenshots of the tables that are numbered.