EDIT: This is in response to this post above:
@imperialdane wrote:
Well this is a bit of an oddity. Had reached the part where i was in the belly of the beast with the probe gun. Got fed up after almost finishing it and having to do the whole thing over again. Saved and left.
When i returned well..
I started quite a bit back (at the area around the junction to the armory and the other warehouse) had to retread the entire trip back. Found i had to build the probe gun again. And also that i had to equip the new probe gun since the old one would not trigger the necessary response.
All in all. Quite confusing.
PC version. Same thing happened to me, but it got compounded with a game-breaking bug:
After everything you said, I advanced back into the belly of the beast. First node, no problem. Shoot it, it pops out, I get rushed by the thin shadow guys with red eyes.
Then I go to find the second node, and none of them work. The probe gun only pings at the slowest rate, even if I point it at the right node (I've watched 10 youtube vids; I know I've got the right one. I also have shot every single probe in the place just to be sure). Nothing happens and I can't progress. I've restarted the area a handful of times.
I found one user complaint buried deep within the gamefaqs forums who had the same problem. He said it eventually magically fixed itself; he kept walking around the area and eventually Isaac started with some dialogue that appears to have triggered the gun pinging again. I walked around every traversible part of the beast for at least 10 mins on three different attempts, to no avail.
This is keeping me from progressing through the game; if this doesn't get fixed my only option will be to start over and HOPE it doesn't happen again. As I am about 50% completion of the storyline, that would be a real drag.