Why are there two different start sites for the tRNA-Gln, for instance:
http://www.ncbi.nlm.nih.gov/nuccore/V00662
tRNA complement(4320..4400)
/product="tRNA-Gln"
http://www.ncbi.nlm.nih.gov/nuccore/NC_012920
tRNA complement(4329..4400)
/gene="TRNQ"
/gene_synonym="MTTQ"
/product="tRNA-Gln"
/note="NAR: 0597"
/anticodon=(pos:complement(4365..4367),aa:Gln)
/codon_recognized="CAA"
/db_xref="GeneID:4572"
/db_xref="HGNC:7495"
/db_xref="MIM:590030"
In addition, mtDNA has indels. The length/coordinate may be different, too (though apparently not in your case). As I remember, there is an indel between GRCh37.p0 and the rCRS strain.
Just FYI, I ran J01415 through tRNAscan-SE (http://lowelab.ucsc.edu/cgi-bin/tRNAscan-SE.cgi) and Rfam (http://rfam.sanger.ac.uk/). I also looked at the pre-computed Rfam result. All three place tRNA-Gln at 4329 - 4400.