The question mark that Eko and John were suppose to find was Jacob's cabin - after all the Pearl is clearly marked to the lower right of the map, not dead centre. Jacob's cabin is the logical place to go to find out what they are suppose to do (in this case to learn to keep pushing the button so that the frieghter cannot find the island).
The Pearl is not clearly marked, there is a question mark after the name. Indicating that they were unsure where The Pearl was. Based on that it was probably Kelvin who put that one in.
The circle (in the question mark design) is meant as an extraction and drop off point for the Pearl's occupants.
Similar circles are found around every stations to provide a 'target' for supply drops.
There are two ?'s on the blast door map: the large one in the center, and a smaller one just above the Pearl Station. The Pearl station was underneath the smaller ?, and the larger ? remains unfound.
The "?" on the blast door map is an expression of something unknown. The "question mark" shape above The Pearl may have no relationship at all to the "?" on the blast door map.
The large "?" on the Blast Door Map actually represents The Barracks. The person drawing the map could not explore the area due to the sonic barrier surrounding it, and hence, assigned a "?" to it.
The dotted line seen surrounding the "?" could represent the sonic barrier as the drawer saw it; an alarm system surrounding the Barracks.
Assuming that Radzinsky was recruited by DHARMA, it doesn't seem plausible that he would have no knowledge of the Barracks, and would therefore not label it on the blast door map as a huge "?".
You know what they say about assuming, though.
Seeing as kelvin was recruited by the true D.I., it would have had to take place between the end of the gulf war, and the purge, so about 1991, since we know Radzinsky was at the swan when kelvin got there, that leads us to the fact that Radzinsky was recruited by the true D.I., not the post purge others D.I.. seeing as he was a member of the true D.I., its obvious that he would have had to have know about the barracks.
Actually the Gulf War started in 1991. So Kelvin was likely recruited after the purge ... wait, what the heck?!
Perhaps Kelvin was recruited by the Others posing as DHARMA, because they needed somebody to stay in the hatch and push the button.
The Question Mark represents an unknown station which Kelvin hasn't heard of. Clearly Kelvin was aware that a station was located there but he didn't know what it was so he marked it with a question mark. This could mean that Radzinsky wasn't the one who marked the question mark in the first place and it would also mean that Kelvin has only ever heard of a few stations such as the Flame and the Medical Staff (as marked on the map) and the reason why he doesn't know of the other stations is because Radzinsky wanted Kelvin to stay in the Hatch and prevent a system failure.