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I had the same issue in regards to where I was started after I saved and quit.  I read the FAQ, it does say it will autosave every 10-15 (approx.).  However, I found that this is not always the case.  I actually got a little further than where you described (I finished the part where the main character is in the belly of the beast) and played a little while after that.  When I saved and quit, I found I was set at the point you described.  This has happened to me more than once, another instance I had to completely repeat nearly an entire clear of an optional mission.  I enjoyed all the Dead Space games, but I am becoming discouraged from playing if I am going to keep getting set back nearly an hour or so every time I save and turn the game off.  I realize it says it only saves your inventory and puts you "near" where you left off.  But this autosave feature doesn't work very well.  I hope the developers fix this autosave feature to either save more often or more accurately start you where you left off.  That or I hope actual save points are reintroduced into the game.

Same issue. 

After several "re-attempts", shut down the console, re-booted, etc., then re-started the game from earlier point to "re-engage" the story line and regain interaction, progress.

End result:  frustrating, but was able to get past the glitch. On the "plus" side, wound up with THREE probe guns (keep one, can dismantle others).

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.

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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.