For me, it's clear that it was indeed MiB. We see the mysterious man in there when Ben and Locke make their first visit, along with a short shot of "the eye". The next time we see the cabin, we see Christian Shepard in there along with "the eye", this is in S4E1 when Hurley runs into the moving cabin. We know from S6E13 that MiB was taking the form of Christian Shepard, and since we also see "the eye", that makes the link with Ben and Locke's visit. Of course, near the end of Season 4 when Locke goes in alone, it's Christian Shepard in there with Claire, who later talked about MiB impersonating her father, making the connection of MiB with the cabin even stronger. In S5 MiB makes Ben admit that he never met Jacob, and that he was "as confused as Locke" about what happened in the cabin. Finally, Ilana and her team go there and she concludes that Jacob "hasn't been there in a long time", the ash circle (which we know keeps the MiB out from S6) has been broken, and "somebody else has been using it".
I would say all the clues are there that we only ever saw MiB in the cabin, although apparently Jacob did use it at some point, with the ash circle in tact to keep MiB away.
It's worth noting that the primary thing MiB uses to get Ben to kill Jacob (and it's easy to forget this because later the focus is on Alex) is Ben's jealousy over his sense that the island, i.e. Jacob, prefers Locke to him. I think that MiB gave his "help me" message only to Locke as an early step in making Ben jealous of Locke, eventually leading Ben to murder Locke, only to have MiB take Locke's form - making Ben even more jealous thinking the island has even resurrected the "chosen" Locke. Then, "Locke" demands to see Jacob and is immediately taken there, while Ben was denied, leading Ben to kill Jacob.