They both align almost perfectly.

 Score =  681 bits (1757),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 331/334 (99%), Positives = 333/334 (99%), Gaps = 0/334 (0%)

Query  9    EEMGSGDYDSIKEPCFREENANFNKIFLPTIYSIIFLTGIVGNGLVILVMGYQKKLRSMT  68
            EEMGSGDYDSIKEPCFREENANFNKIFLPTIYSIIFLTGIVGNGLVILVMGYQ+KLRSMT
Sbjct  1    EEMGSGDYDSIKEPCFREENANFNKIFLPTIYSIIFLTGIVGNGLVILVMGYQEKLRSMT  60

Query  69   DKYRLHLSVADLLFVITLPFWAVDAVANWYFGNFLCKAVHVIYTVNLYSSVLILAFISLD  128
            DKYRLHLSVADLLFVITLPFWAVDAVANWYFGNFLCKAVHVIYTVNLYSSVLILAFISLD
Sbjct  61   DKYRLHLSVADLLFVITLPFWAVDAVANWYFGNFLCKAVHVIYTVNLYSSVLILAFISLD  120

Query  129  RYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFGNVSEADDRYICDRFYPND  188
            RYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIF NVSEADDRYICDRFYPND
Sbjct  121  RYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFANVSEADDRYICDRFYPND  180

Query  189  LWVVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGHQKRKALKTTVILILAFFACWL  248
            LWVVVFQFQHIMVGLILPGIV+LSCYCIIISKLSHSKGHQKRKALKTTVILILAFFACWL
Sbjct  181  LWVVVFQFQHIMVGLILPGIVMLSCYCIIISKLSHSKGHQKRKALKTTVILILAFFACWL  240

Query  249  PYYIGISIDSFILLEIIKQGCEFENTVHKWISITEALAFFHCCLNPILYAFLGAKFKTSA  308
            PYYIGISIDSFILLEIIKQGCEFENTVHKWISITEALAFFHCCLNPILYAFLGAKFKTSA
Sbjct  241  PYYIGISIDSFILLEIIKQGCEFENTVHKWISITEALAFFHCCLNPILYAFLGAKFKTSA  300

Query  309  QHALTSVSRGSSLKILSKGKRGGHSSVSTESESS  342
            QHALTSVSRGSSLKILSKGKRGGHSSVSTESESS
Sbjct  301  QHALTSVSRGSSLKILSKGKRGGHSSVSTESESS  334

The shift comes from the fact that those sequences were extracted from a partial RNA:

gi:7230482 is coded by a partial DNA : http://www.ncbi.nlm.nih.gov/nuccore/7230481

gi:9587714 is also coded by a partial cds : http://www.ncbi.nlm.nih.gov/nuccore/AF172229.1

These can be two variants of same gene: As the title says one is CXCR4 homologues of gibbon ape. Other possibility may be use of different start sites.

CLUSTAL 2.0.12 multiple sequence alignment

AAF89349.1      IYTSDNYTEEMGSGDYDSIKEPCFREENANFNKIFLPTIYSIIFLTGIVGNGLVILVMGY
AAF42991.1      --------EEMGSGDYDSIKEPCFREENANFNKIFLPTIYSIIFLTGIVGNGLVILVMGY
                        ****************************************************

AAF89349.1      QKKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANWYFGNFLCKAVHVIYTVNLYSSVL
AAF42991.1      QEKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANWYFGNFLCKAVHVIYTVNLYSSVL
                *:**********************************************************

AAF89349.1      ILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFGNVSEADDRYI
AAF42991.1      ILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFANVSEADDRYI
                *************************************************.**********

AAF89349.1      CDRFYPNDLWVVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGHQKRKALKTTVILI
AAF42991.1      CDRFYPNDLWVVVFQFQHIMVGLILPGIVMLSCYCIIISKLSHSKGHQKRKALKTTVILI
                *****************************:******************************

AAF89349.1      LAFFACWLPYYIGISIDSFILLEIIKQGCEFENTVHKWISITEALAFFHCCLNPILYAFL
AAF42991.1      LAFFACWLPYYIGISIDSFILLEIIKQGCEFENTVHKWISITEALAFFHCCLNPILYAFL
                ************************************************************

AAF89349.1      GAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVSTESESSSFHSS
AAF42991.1      GAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVSTESESS-----
                ******************************************

They came from different labs:

AF178083_1 --> Department of Biology, California State University, Northridge (provides link to publication)

AF172229_1 --> Lab of Cellular and Molecular Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences (unpublished data)

Accordingly, my guess is that they probably come from different samples. Just like most human genes have variations, these probably came from different individual gibbons (with slightly different versions of the gene)