I am working from the following version of code:

HDecode Version:
char *hdecode_version = "!HVER!HDecode:   3.4 [GE 25/04/06]";
char *hdecode_sccs_id = "$Id: HDecode.c,v 1.1.1.1 2006/10/11 09:54:55
jal58 Exp $";

Following are the diffs for fixes. I have not tested the part of the
fixes that are used for aligning from a label file (-R option).

HDecode.c

735c735
< BestInfo *FindLexNetLab (MemHeap *heap, LexNode *ln, LLink ll)
---
> BestInfo *FindLexNetLab (MemHeap *heap, LexNode *ln, LLink ll, HTime
frameDur)
757c757
<             next = FindLexNetLab (heap, follLN, ll->succ);
---
>             next = FindLexNetLab (heap, follLN, ll->succ, frameDur);
761,762c761,762
<                info->start = ll->start / 1.0e5;
<                info->end = ll->end / 1.0e5;
---
>                info->start = ll->start / (frameDur*1.0e7);
>                info->end = ll->end / (frameDur*1.0e7);
772c772
<          next = FindLexNetLab (heap, follLN, ll);
---
>          next = FindLexNetLab (heap, follLN, ll, frameDur);
776c776
<             info->start = info->end = ll->start / 1.0e5;
---
>             info->start = info->end = ll->start / (frameDur*1.0e7);
788c788
< BestInfo *CreateBestInfo (MemHeap *heap, char *fn)
---
> BestInfo *CreateBestInfo (MemHeap *heap, char *fn, HTime frameDur)
828,829c828,829
<    bestAlignInfo->start = ll->start / 1.0e5;
<    bestAlignInfo->end = ll->end / 1.0e5;
---
>    bestAlignInfo->start = ll->start / (frameDur*1.0e7);
>    bestAlignInfo->end = ll->end / (frameDur*1.0e7);
835c835
<    bestAlignInfo->next = FindLexNetLab (&transHeap, ln, ll->succ);
---
>    bestAlignInfo->next = FindLexNetLab (&transHeap, ln, ll->succ,
frameDur);
927,930d926
< 
<    /* get transcrition of 1-best alignment */
<    if (bestAlignMLF)
<       bestAlignInfo = CreateBestInfo (&transHeap, fn);
940a937,940
> 
>    /* get transcrition of 1-best alignment */
>    if (bestAlignMLF)
>       bestAlignInfo = CreateBestInfo (&transHeap, fn,
pbInfo.tgtSampRate/1.0e7);
1043c1043
<            cpuSec, frameN/100.0, cpuSec / (frameN/100.0));
---
>            cpuSec, frameN*dec->frameDur, cpuSec /
(frameN*dec->frameDur));

HLVRec-traceback.c

247c247
<          printf ("   n %d t %.3f W %s\n", (int) path->user,
path->frame / 100.0, s);
---
>          printf ("   n %d t %.3f W %s\n", (int) path->user,
path->frame * dec->frameDur, s);
278c278
<       ln->time = path->frame / 100.0;   /* fix frame duration! */
---
>       ln->time = path->frame * dec->frameDur;
293c293
<          printf ("I=%d t=%.2f W=%d\n", n, path->frame/100.0,
path->pron);
---
>          printf ("I=%d t=%.2f W=%d\n", n, path->frame*dec->frameDur,
path->pron);
635c635
<       if (fabs (dur - laDur > dec->frameDur/2))
---
>       if (fabs (dur - laDur ) > dec->frameDur/2)