Excessively inefficient source code modifications

Hello,

I've made some changes in the libvorbis-1.2.3 source code to introduce
some functionality I need for a project I'm working on. For compilation,
besides including some macro definitions I need to pass to the C
preprocessor, and linking with the math library somewhere (and including
the source files I've implemented, of course) I've made no big changes
in the Makefile or configure scripts. But when I run my modified oggenc
program, the execution time becames excessive (for coding 2 secs of
audio it spents approximately 2 mins, with default parameters). The
modifications I've made consist basically in some extra computation
involving the residual vectors (so it executes once for each residue
vector). I've measured independently the average time for the whole
extra code and it takes approximately 0.00012 secs per call (so that
would make roughly 0.00012*channels*frames extra encoding time for an
audio file). Despite I've re-re-rechecked my code and I haven't found
anything strange, I don't discard at all that may be there are some
algorithmic errors left that may make my code be a bit inefficient, but
making 2 secs go to 2 mins is quite alarming and far away from
permissible. Supposing I have no important algorithmic errors, could
this excessive overload be caused by a compiling issue? (that wouldn't
surprise me, as my knowledge about autoconf/automake/make scripts is
quite basic...).

I'd just like to discard the fact of having a compilation issue before
starting another intensive and detailed analysis of the code. If after
another bunch of extra hours and thousands of code lines rechecked, I
find that it was a compilation issue, I might be forced to make a
pilgrimage to the Himalayas to find myself or something... ;)

Thank you all.