[Kaldi-users] timings don't match decoding

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Following the formal s5 scripts in wsj and the directions below, I was able to get word timings that ROUGHLY matched the decoding values I was getting.   

in the decode file (20.txt , decoding with a beam of 20) :

02.cut1 YOU ARE STANDING ON A SANDY WHITE BEACH OF THE ASSISTED AND END A THAN ANY OTHER KIND CONSISTED . . . 

in the timings.all.txt file:
02.cut1 1 2.64 0.03 <UNK> 
02.cut1 1 3.06 0.11 YOU 
02.cut1 1 3.17 0.22 ARE 
02.cut1 1 3.39 0.40 STANDING 
02.cut1 1 4.06 0.23 ON 
02.cut1 1 4.29 0.06 A 
02.cut1 1 4.35 0.12 IS 
02.cut1 1 4.57 0.75 INVIOLATE 
02.cut1 1 5.43 1.24 ECOSYSTEM 
02.cut1 1 6.88 0.35 NESTS 
02.cut1 1 7.64 0.65 ASSISTED(2) 
02.cut1 1 8.29 0.19 OUT 
02.cut1 1 9.76 1.06 ENLISTED(2) 
02.cut1 1 10.82 0.41 WOULD 
02.cut1 1 11.23 0.59 AN 
02.cut1 1 11.82 0.79 ALAN'S 
02.cut1 1 12.67 1.03 NETTLESOME 
02.cut1 1 13.84 1.00 INSISTED 
02.cut1 1 14.84 0.21 AND 

Here are the commands:

%utils/mkgraph.sh data/local/g300_test/lang exp/tri1 exp/tri1/graph
%steps/decode.sh --nj 10 --model exp/tri1/final.mdl --num-threads 1 --acwt 0.1 --cmd "$decode_cmd" --config conf/decode.config exp/tri1/graph data/local/g300_test exp/tri1/decode_g300_test
%lattice-1best "ark:gunzip -c exp/tri1/decode_g300_test/lat.*.gz|" ark:- | lattice-align-words ./data/local/g300_test/lang/phones/word_boundary.int exp/tri1/final.mdl ark:- ark:- | nbest-to-ctm ark:- - | ./utils/int2sym.pl -f 5 ./data/local/g300_test/lang/words.txt > exp/tri1/decode_g300_test/timings.all.txt
LOG (lattice-1best:main():lattice-1best.cc:88) Done converting 339 to best path, 0 had errors.
LOG (lattice-align-words:main():lattice-align-words.cc:117) Successfully aligned 339 lattices; 0 had errors.
LOG (nbest-to-ctm:main():nbest-to-ctm.cc:95) Converted 339 linear lattices to ctm format; 0 had errors.

It should use the lattices generated from the decoding and the word_boundary and word files.   I can apply weights for language model and acoustic model, but I doubt that will have a great effect.   The words.txt file must be correct if I am getting "similar" results.   

Anyway, any help is appreciated.  

Nathan