I recently installed IDE 1.6.5 and find that the compiler always does a complete rebuild, regardless of whether or not anything has changed. Even compiling an empty sketch takes 30 seconds.
In viewing the forum notes, I see that this is indicated as "fixed" in 1.6.0 (or close to that number...don't have it before me at the moment). I also recall a discussion around the fact that the compiler's pathnames included both '/' and '' in the same path; and that spaces in the pathname could cause problems.
My compile output does not list any errors, but is full of mixed forward-backward slashes, and places temp files in my user directory, which does contain spaces. Not sure if this is related to the issue, but this is really disappointing to see this persist in the latest version.
Example line from compiler output:
C:\Arduino\hardware\tools\avr/bin/avr-g++ -c -g -Os -w -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics -MMD -mmcu=atmega328p -DF_CPU=16000000L -DARDUINO=10605 -DARDUINO_AVR_UNO -DARDUINO_ARCH_AVR -IC:\Arduino\hardware\arduino\avr\cores\arduino -IC:\Arduino\hardware\arduino\avr\variants\standard C:\Arduino\hardware\arduino\avr\cores\arduino\abi.cpp -o C:\Users\DONALD~1\AppData\Local\Temp\build298671727825666574.tmp\abi.cpp.o