One problem is:
-0.04166667 'bnstfq' = number of days between baro nesting archive input
-0.04166667 'nestfq' = number of days between 3-d nesting archive input
The negative sign indicates the input is mean archives (archm files), but you actually have snapshot archives (archv files):
ln -sf /storage/home/hcoda1/6/jkim3990/scratch/HYCOM-examples/FLCa0.01/expt_01.2/../datasets/subregion/archv.2011_001_01.a archm.2011_001_01.a
The nesting program can read either kind of archive with either naming convention, but the reason both are allowed is because mean archives are nominally at the midpoint of their span. So daily means are nominally at 12Z and daily snapshots are at 00Z. So setting nestfq negative indicates that the archive is archm and its date is for a mean.
There is no such thing as hourly means because they should nominally be in the center of each hour and HYCOM's archives don't include the minutes (always 0 minutes into the hour). So I'm not sure what setting nestfq to minus one hour actually does.
Since you have archv files, change to:
0.04166667 'bnstfq' = number of days between baro nesting archive input
0.04166667 'nestfq' = number of days between 3-d nesting archive input
And keep the original archv name.
I don't know if this is the only issue, but see if this helps.
Since you have hourly nesting files, the e-folding time could be less than 0.1 days:
W, E boundaries: 80 grid pts with 0.1-9 day e-folding time
Typically signals longer than 5x the e-folding time will be reproduced.
Or you could reduce the reading load by reading every 3 hours (say)
0.04166667 'bnstfq' = number of days between baro nesting archive input
0.125 'nestfq' = number of days between 3-d nesting archive input
Alan.