I'm using an older version of Access, without the pdf output add-in that you refer to. We currently use a third party pdf printer driver, but in the past we have used the older "snapshot" output. Because of the difference in versions, I don't know if this will have any bearing on your problem, but we had a similar issue when using the snapshot output and perhaps our work-around will also work for you.
Regardless of whether we printed or used the output command, Access still appeared to use the page margins as set in Page Setup. I think it uses the greater of the margins set in the report/form and the margins set in Page Setup. If you find that your output is fine some of the time, and not others, it may be because the default page margins differ either from PC to PC or from user to user. We had few users and few PCs, so we set them all to the same settings manually, but you may be able to add code to your script to set the page margins (the .Left, .Width, .Top and .Height properties apply to a form or report but I don't think they actually override the default page margins).
Furthermore, we found that some of the output formats seemed to add their own margin in addition to the default margin. This resulted in an overwide top and left margin, which could result in truncation of the right and bottom of the output. Our solution was to set the Access page setup top and left margins to zero, and right and bottom margins to the total of the margins we wanted. Unfortunately the resulting output was not always centred on the page, but at least it didn't get truncated.