For a full resolution still photo (60D: 18MP), usually around 25 seconds on a 2012 Macbook Air (1.8GHz i5). If it only takes 2 seconds to process that probably means cr2hdr thought it wasn't dual ISO and didn't try to process it (or maybe you are working with video at a much lower resolution?). I would suggest looking at the output from cr2hdr.
david$ time ./cr2hdr /Volumes/EXTHD/ML/Misc/dual\ iso\ test/DUAL7313.CR2
cr2hdr: a post processing tool for Dual ISO images
Last update: 76b5a32 on 2015-03-21 15:19:29 UTC by david:
dng: allow 64 bit compilation for raw2dng, mlv_dump, and cr2hdr
Active options:
--amaze-edge : use a temporary demosaic step (AMaZE) followed by edge-directed interpolation (default)
--cs2x2 : apply 2x2 chroma smoothing in noisy and aliased areas (default)
Input file : /Volumes/EXTHD/ML/Misc/dual iso test/DUAL7313.CR2
Camera : Canon EOS 60D
Full size : 5344 x 3516
Active area : 5202 x 3465
White level : 12500
Black borders : 142 left, 51 top
Black level : 1966
ISO pattern : dBBd GBRG
Noise levels : 5.99 18.13 18.96 5.98 (14-bit)
ISO difference : 4.00 EV (1603)
Black delta : 3.74
Dynamic range : 10.78 (+) 9.12 => 13.12 EV (in theory)
Looking for hot/cold pixels...
Hot pixels : 2
Cold pixels : 26
AMaZE interpolation ...
Amaze took 4.31 s
Edge-directed interpolation...
Semi-overexposed: 3.97%
Deep shadows : 72.60%
Horizontal stripe fix...
Full-res reconstruction...
ISO overlap : 3.8 EV (approx)
Half-res blending...
Chroma smoothing...
Building alias map...
Filtering alias map...
Smoothing alias map...
Final blending...
Noise level : 4.03 (16-bit), ideally 4.01
Dynamic range : 13.35 EV (cooked)
Black adjust : 2
White balance determined from WB_RGGBLevelsMeasured
AsShotNeutral : 0.774398 1 0.437742
Output file : /Volumes/EXTHD/ML/Misc/dual iso test/DUAL7313.DNG
1 image files updated
real 0m26.715s
user 0m22.857s
sys 0m1.359s
here I deliberately ran it on a non dual ISO image, took around 3 seconds:
david$ time ./cr2hdr /Volumes/EXTHD/ML/Misc/dual\ iso\ test/IMG_7312.CR2
cr2hdr: a post processing tool for Dual ISO images
Last update: 76b5a32 on 2015-03-21 15:19:29 UTC by david:
dng: allow 64 bit compilation for raw2dng, mlv_dump, and cr2hdr
Active options:
--amaze-edge : use a temporary demosaic step (AMaZE) followed by edge-directed interpolation (default)
--cs2x2 : apply 2x2 chroma smoothing in noisy and aliased areas (default)
Input file : /Volumes/EXTHD/ML/Misc/dual iso test/IMG_7312.CR2
Camera : Canon EOS 60D
Full size : 5344 x 3516
Active area : 5202 x 3465
Doesn't look like interlaced ISO
real 0m3.126s
user 0m2.667s
sys 0m0.255s
Watching the output to see how long various things take may give you some clues, cr2hdr even tells you exactly how long AMaZE interpolation takes.