No, this is the same sequence. A single RefSeq accession will correspond to one sequence. However, nobody said that sequence needs to be unique in the genome. The specific sequence you are talking about, NM_001085545.1, is a mouse transcript which can be aligned to many different regions of the mouse's chromosome X.
This is your sequence:
>NM_001085545.1
agagaagtctaggcaggactggcagactacagcaatgcctcaaccaagaagcctctgcga
gagcttgttctaggaattttcatcaatggggcttttagtcagcagggtcttgagatgcag
ggattccagtctgttagagccacagccagaagccatagccggagccagctacattcctgg
cagtcgcaagcgaaaaagaaacagtttggaggagttggcaacaagttctaatgttcatgg
acctcaaaaccagggaatgtatccacatcaagttctcaactacatctactggaaaagggt
taagatctcatctaatgatgcttatcaaaacttatttttggacgggcatgatagcgacat
taaaatccgtgctctgggaaaaacatggtgtttacacaaagtatttttatgtcagtcagg
ctactttgctaacattctcaaaggtacttggagagaatcacaccatggtgttataaatct
gatcattaagaatgaggatattgatacccgatctctgcattttgtgtttggtgctttgta
cacggatgcggatttgtcaataacacctctggaagttcctcaagttttggcagcagcatg
cctgcttcgggtggatcaagtaattcagcagtgtgaaggaatcatgaaagaaactatcaa
caggaacactgtgtgctcctattatttggcagcagaaacctatagattaaaagctgtaaa
gacgagatgctttgaatggcttctttgcaatttgatggtacatccaagtgtggcacttta
caaggaagtagacttgaagttgatgtatcttctagcactgtcttctgacttactagtcat
gcaaaaggagattgatgtatataccacactaaaaatatggatgttcctttatcttaatcc
atgctggaacggaaccatgaaacagcttttacaacacgcaaacaactggctttccaccca
catggcatatgttgataacatcagttttcttgaaagtgaagaaggactaatatttcaacc
agtgtttaaaaagctgagatttcagcacattatctgtgacttgacttccacaactattct
tgaacaagatcgactaatacctatggcatggttgtcacccatttacaaacaacagtggtt
gactttgctgcgaacacaagaatatggggtaattggaccacaagttatcaatgaacaaga
acttgaagaatgcaccatgaggtgtggtacaatgatccccaaggatggaagatatacttg
gaagtggtcagttggacgacttggctttcctttacgtgtgacctttaccaggcagtgtgt
aattttaaggcaacggtgtcagaggtgtgatggttctgcttgccacaaccatatccgaaa
tgtcatattcagaataactttggtgtgttttgattccaacaaaagagtaactttcagaaa
gacaacaggttataaaatcctcacctttgaatataaggaggagcaaattgtaatgaaatt
ggatagtgatgttctaaccttccctatgtgtatattctgcaatttcctttttgtaaacct
aggaaatgcagaaaacaagtaatcttatcaattattagactgtaagtattttacaagtat
tgaatggttcatttaatatgaaggctgtgtaatgactacagtgaagaagaccaaaaacaa
attcaatattctttggagtctagtaccaccagaagtgactgcttccctccatcaccttat
ttccatgtatttctgaagaaaacctttacttccaacaaagtatttgtcaaatcaaataaa
cctaatcttctgatttaaatttaccatcgagatccaagcttggaatggaaataagagact
atatttgcaaggtaaaacatctcaatcaatttgttaagtagatttggccctagctaaaat
tgagacaaaataaaatcatgccattgttgaaactgttgtg
If you BLAT it against the mouse genome using the UCSC BLAT tool, you will see many hits, most of them almost perfect matches and some of them overlapping the regions given in your bed file:

Your bed file matches the following hits in the image above:
NM_001085545.1 1954 1 1960 1960 99.9% chrX - 3441731 3443690 1960
NM_001085545.1 1960 1 1960 1960 100.0% chrX + 3700233 3702192 1960
NM_001085545.1 1954 1 1960 1960 99.9% chrX - 3750926 3752885 1960
NM_001085545.1 1954 1 1960 1960 99.9% chrX + 31336369 31338328 1960
I don't know why your bed file has all of these various matches for NM_001085545.1, since you haven't told us what the bed file is supposed to be doing. A bed file is just a collection of regions. For all I know, that bed file is just "a few hits for sequence NM_001085545.1 in the genome". There is no reason to assume that each region in a bed file corresponds to a gene.
So there's nothing wrong with your file, you're just dealing with a non-unique sequence from the mouse genome. And you don't have multiple sequences with the same accession, you have one sequence, one accession, but multiple hits for that sequence in the genome.