Tracy:
I have used and applied a lot of dip pipes as tank fill lines - especially on projects for companies like DuPont, ExxonMobil, Huntsman, etc., etc. The hole drilled into the dip pipe's side, directly under the tank roof is, of course, to break a potential syphoning effect. And it works! The holes I employ are 3/8" in diameter for 2" - 4" pipe - which are some of your more common sizes. If you have viscous, slurries, or fluids that tend to cover the hole, then a larger size may be called for on the larger sizes of dip pipe. But I've never had any syphoning taking place with the drilled hole in place.
Bear in mind that some "line pack" may dribble back, depending on your piping configuration. The usual configuration is to install the flanged, fill nozzle directly on the tank (or vessel) roof and insert the dip pipe inside this nozzle (with a slip-on flange welded to it at the appropriate depth) and bolt the two flanges together, fixing the dip pipe to the nozzle and to a pre-set depth. Under this configuration you will have some degree of liquid fluid remaining in the fill line all the way up to the height where the fill line makes a 180o turn to enter the dip pipe. This could be the liquid that you identify as "syphoning back", but in reality it is draining back by gravity and not by a syphoning effect. Could this be the answer to your dilemma?
Perhaps the above doesn't address what you describe, because I've only described a generic type of dip pipe for filling purposes. What your description doesn't mention is what you are using the dip pipe for. You say you inadvertently pulled a vacuum on the vessel and had liquid drawn into the vacuum pump. If your vacuum pump is the instrument pulling the vacuum and it was being done using the dip pipe for vacuum draw, then you can pull liquid up through the dip pipe if the diameter of the vacuum breaker hole is not big enough. Your vacuum draw may be so fast that you establish sonic flow through the orifice hole and this maximizes the amount of gas that can be pulled through there - and it may not be enough. Therefore, the vacuum draw would start to "raise" the level of the liquid in the dip pipe and possibly defeat the 180o turn at the top of the tank, and drain down the fill line by gravity. This could be another explanation to your dilemma.