Thanks for your ideas Dennis. Some answers:
1) I'm using SlickEdit v 11.0.1 currently, but I've seen essentially this same set of problems at least back through v. 9. Maybe further - I've been using SlickEdit for at least a decade, so some of my experiences are lost in the mists of time
2) The application is local. I always attach the debugger to it once it is running (Attach to running process using GDB).
3) Typically, the stack on the main thread is a dozen or less levels deep.
4) The application is large, not sure what you're interested in. Typically at rest (waiting for input), on an amd64bit machine, it has a virtual size of 1.6 gig or so, but the vast majority of that is data, not code segment.
As I noted in my first post, the version of gdb that ships with SlickEdit complains about our file format (presumably because I'm working on an amd64 machine), so I use the one we have in-house, which is 6.3 for 64 bit suse linux.
Your remark about using path and filename makes sense, but this is what gdb seems to be objecting to. Note that SlickEdit seems to be giving only the last part of the path (e.g. bar/foo.c), rather than the entire path. As I mentioned, if I run gdb directly at the xterm command line and try to set a breakpoint using a partial path and filename, it gives me the same error message that SlickEdit eventually returns to me. So it seems that, at least for this version of gdb, a partial path and filename isn't accepted (perhaps there's some setting in gdb that I can change? I looked through as much of the help as seemed relevant, but didn't find anything).
This is a problem if I try to set a breakpoint in the margin of the source. But I can set breakpoints by clicking on the add breakpoint icon in the breakpoints window IF I choose the first line of a function (it seems it's setting the breakpoint by function name rather than by line number in that case).
In all cases, the response when setting a breakpoint is usually (but not always) extremely slow. Oddly enough, "top" doesn't show the time being taken either by SlickEdit or by gdb. In fact, they are using 0.0 %CPU. It's almost as if they are blocked on something else. The main user of CPU time continues (as always) to be the command shell - in fact, as long as I don't do anything else, it and top are essentially the only CPU users.
If SlickEdit is communicating with gdb through the MI interface, I note that at least in the latest documentation, breakpoint-insert commands seem to take only the filename (and return to you the full path, which I supposed can be used as a check). It certainly isn't clear what gdb does if there are two files with the same name.