I had/have the same problem like you (have a look at my last post from today evening CET).
Since i am starting the script over a webapp written in php, after i realized that changing indesign user interaction doesn't solve this, i had to allow the script and Indesign interact with the desktop before i could see what kind of message appears in the dialog.
although i am not shure if changeing InDesigns user interaction would beware my script from beeing stopped by dialog boxes in the future, in this case it was a wscript/cscript dialog box that stopped my script.
What message appears in your dialog box?
In my case it's definitely an InDesign dialog box telling that the linked image files and sometimes fonts can't be found. This is normal since I don't have the corresponding files on my computer.
With some files, the dialog is desactivated and my script works well but with others I still have the dialog box showing up, which stops the script. I found out, that in the file on which this "error" occurs, I have i.e. 24 missing files when opening the document "manually" in InDesign and only 4 left when I open it through the script...
One solution would be to ignore the link check (like asking not to repair the links when you open the file "manually"), but I didn't find any solution for that.
The template file i am opening with vbscript has about 10 different broken links to picture. i stopped figuring out that problem as soon as i realized that disabling the user interaction doesn't handle this kind of dialog and pointed indesign to the right location where the images are stored on the network.
i don't know any feature that disablelink check when opening files in ID. DataMerge Funktion has an option that warns if a link to a merged image is broken, also i think i saw that you can tell the script to handle different types of dialogs (message, warnings...) by the userinteract property.
perhaps you can figure out some differences between broken links to images that stopped your script and the ones that did not?