It looks like you're not the only one with this issue.
I understand that your code is already setup and you want to run with what you have, but unless someone comes up with a hack or Google decided to fix what is clearly a bug, I think you need to re-think how you are approaching this issue.
If chromeless windows were an option, or if the print dialogue were a modal then you could pull this off with the current strategy, but neither of those options are possible in Chrome. Even if you were able to get around this scrolling issue somehow you're still left with a less than desirable UX problem in that if the user hits "cancel" in the print dialogue then they are left with a still open blank window.
Here is a JS fiddle to demonstrate that you need to change your approach: DEMO
You can see from this demonstration that even if we run a completely separate script from within the new window by passing it as plain text in the content object, it still causes the same issue. This means to me that this is a parent/child type of a relationship that is not easily circumvented with JS.
I recommend 2 alternative possible solutions:
Option1:
<input type="button" value="Print" onclick="window.print(); return false;" />
This triggers a full screen print dialogue that can't be closed from the "Windows Close Button." That way you can avoid the issue all together. Then you can use a combination of JS and Print Styles to target and isolate the information you want to print. I know it's more work but I think may be the better cross-platform solution.
This option is more brute force and simplistic in nature (and you have already commented that you know this but I'm leaving it up because it's still an option).
DEMO
Option2:
- User clicks on a link/button that opens a new tab/window
- In the same function the data from your table gets loaded into a JSON Object
- The JSON object is loaded into a print template in the new tab/window
- the template initiates the print function
By taking these actions, I think you will have disassociated the JS instance enough that the new tab will not affect the initiating script.