Patch taken from upstream powertop 1.13 is attached which solves this problem.
--- powertop-1.11/config.c 2008-12-30 19:52:54.000000000 +0100 +++ powertop-1.13/config.c 2010-07-20 01:08:21.000000000 +0200 @@ -33,7 +33,8 @@ #include "powertop.h" /* static arrays are not nice programming.. but they're easy */ -static char configlines[5000][100]; +#define MAXCONFIGLINES 10000 +static char configlines[MAXCONFIGLINES][100]; static int configcount; static void read_kernel_config(void) @@ -49,6 +50,8 @@ char line[100]; if (fgets(line, 100, file) == NULL) break; + if (configcount >= MAXCONFIGLINES) + break; strcpy(configlines[configcount++], line); } pclose(file); @@ -77,6 +80,8 @@ char line[100]; if (fgets(line, 100, file) == NULL) break; + if (configcount >= MAXCONFIGLINES) + break; strcpy(configlines[configcount++], line); } fclose(file);