FFmpeg is a great option.  I've done it many times myself with time lapse photography experiments. 
- Install FFmpeg with x264 CODEC
- Number all your slides starting at 0001.jpg
- Run FFmpeg like below (this is what I use for my images-->video conversions):
FFmpeg command:
ffmpeg -f image2 -i %04d.jpg -vcodec libx264 -f mp4 -vpre main -vpre normal \
   -r 25 -an -threads 4 -b 3000k -mbd rd -flags +mv4+aic -trellis 2 -cmp 2 \
   -subcmp 2 -g 300 -y out.mp4
You may need to tinker with the command line to get the desired output quality you are searching for.  Also, the frame rate (-r 25) is probably too high for you.  Either experiment with small values, or duplicate your slides programmatically.