No, I don't have a problem after reboot. If I reconnect usb cable, GPS work fine.Do you really only have this problem after rebooting?
For me it looks like a general problem of your device!
List usb devices after reboot:
root@jacinto6evm:/ # cat /sys/kernel/debug/usb/devices
T: Bus=04 Lev=00 Prnt=00 Port=00 Cnt=00 Dev#= 1 Spd=5000 MxCh= 1
B: Alloc= 0/800 us ( 0%), #Int= 0, #Iso= 0
D: Ver= 3.00 Cls=09(hub ) Sub=00 Prot=03 MxPS= 9 #Cfgs= 1
P: Vendor=1d6b ProdID=0003 Rev= 3.14
S: Manufacturer=Linux 3.14.57-00147-gb164ce2 xhci-hcd
S: Product=xHCI Host Controller
S: SerialNumber=xhci-hcd.1.auto
C:* #Ifs= 1 Cfg#= 1 Atr=e0 MxPwr= 0mA
I:* If#= 0 Alt= 0 #EPs= 1 Cls=09(hub ) Sub=00 Prot=00 Driver=hub
E: Ad=81(I) Atr=03(Int.) MxPS= 4 Ivl=256ms
T: Bus=03 Lev=00 Prnt=00 Port=00 Cnt=00 Dev#= 1 Spd=480 MxCh= 1
B: Alloc= 0/800 us ( 0%), #Int= 0, #Iso= 0
D: Ver= 2.00 Cls=09(hub ) Sub=00 Prot=01 MxPS=64 #Cfgs= 1
P: Vendor=1d6b ProdID=0002 Rev= 3.14
S: Manufacturer=Linux 3.14.57-00147-gb164ce2 xhci-hcd
S: Product=xHCI Host Controller
S: SerialNumber=xhci-hcd.1.auto
C:* #Ifs= 1 Cfg#= 1 Atr=e0 MxPwr= 0mA
I:* If#= 0 Alt= 0 #EPs= 1 Cls=09(hub ) Sub=00 Prot=00 Driver=hub
E: Ad=81(I) Atr=03(Int.) MxPS= 4 Ivl=256ms
T: Bus=03 Lev=01 Prnt=01 Port=00 Cnt=01 Dev#= 2 Spd=480 MxCh= 3
D: Ver= 2.01 Cls=09(hub ) Sub=00 Prot=02 MxPS=64 #Cfgs= 1
P: Vendor=0424 ProdID=4502 Rev= 1.85
C:* #Ifs= 1 Cfg#= 1 Atr=e0 MxPwr= 2mA
I: If#= 0 Alt= 0 #EPs= 1 Cls=09(hub ) Sub=00 Prot=01 Driver=hub
E: Ad=81(I) Atr=03(Int.) MxPS= 1 Ivl=256ms
I:* If#= 0 Alt= 1 #EPs= 1 Cls=09(hub ) Sub=00 Prot=02 Driver=hub
E: Ad=81(I) Atr=03(Int.) MxPS= 1 Ivl=256ms
T: Bus=03 Lev=02 Prnt=02 Port=02 Cnt=01 Dev#= 3 Spd=480 MxCh= 0
D: Ver= 2.00 Cls=00(>ifc ) Sub=00 Prot=00 MxPS=64 #Cfgs= 1
P: Vendor=0424 ProdID=2530 Rev= 1.16
S: Product=Bridge device
C:* #Ifs= 1 Cfg#= 1 Atr=c0 MxPwr= 0mA
I:* If#= 0 Alt= 0 #EPs= 0 Cls=ff(vend.) Sub=ff Prot=ff Driver=(none)
T: Bus=02 Lev=00 Prnt=00 Port=00 Cnt=00 Dev#= 1 Spd=5000 MxCh= 1
B: Alloc= 0/800 us ( 0%), #Int= 0, #Iso= 0
D: Ver= 3.00 Cls=09(hub ) Sub=00 Prot=03 MxPS= 9 #Cfgs= 1
P: Vendor=1d6b ProdID=0003 Rev= 3.14
S: Manufacturer=Linux 3.14.57-00147-gb164ce2 xhci-hcd
S: Product=xHCI Host Controller
S: SerialNumber=xhci-hcd.0.auto
C:* #Ifs= 1 Cfg#= 1 Atr=e0 MxPwr= 0mA
I:* If#= 0 Alt= 0 #EPs= 1 Cls=09(hub ) Sub=00 Prot=00 Driver=hub
E: Ad=81(I) Atr=03(Int.) MxPS= 4 Ivl=256ms
T: Bus=01 Lev=00 Prnt=00 Port=00 Cnt=00 Dev#= 1 Spd=480 MxCh= 1
B: Alloc= 0/800 us ( 0%), #Int= 0, #Iso= 0
D: Ver= 2.00 Cls=09(hub ) Sub=00 Prot=01 MxPS=64 #Cfgs= 1
P: Vendor=1d6b ProdID=0002 Rev= 3.14
S: Manufacturer=Linux 3.14.57-00147-gb164ce2 xhci-hcd
S: Product=xHCI Host Controller
S: SerialNumber=xhci-hcd.0.auto
C:* #Ifs= 1 Cfg#= 1 Atr=e0 MxPwr= 0mA
I:* If#= 0 Alt= 0 #EPs= 1 Cls=09(hub ) Sub=00 Prot=00 Driver=hub
E: Ad=81(I) Atr=03(Int.) MxPS= 4 Ivl=256ms
T: Bus=01 Lev=01 Prnt=01 Port=00 Cnt=01 Dev#= 2 Spd=480 MxCh= 4
D: Ver= 2.01 Cls=09(hub ) Sub=00 Prot=02 MxPS=64 #Cfgs= 1
P: Vendor=0424 ProdID=4913 Rev= 8.00
S: Manufacturer=Microchip Tech
S: Product=USB4913
C:* #Ifs= 1 Cfg#= 1 Atr=e0 MxPwr= 0mA
I: If#= 0 Alt= 0 #EPs= 1 Cls=09(hub ) Sub=00 Prot=01 Driver=hub
E: Ad=81(I) Atr=03(Int.) MxPS= 1 Ivl=256ms
I:* If#= 0 Alt= 1 #EPs= 1 Cls=09(hub ) Sub=00 Prot=02 Driver=hub
E: Ad=81(I) Atr=03(Int.) MxPS= 1 Ivl=256ms
T: Bus=01 Lev=02 Prnt=02 Port=00 Cnt=01 Dev#= 5 Spd=12 MxCh= 0
D: Ver= 1.10 Cls=02(comm.) Sub=00 Prot=00 MxPS=64 #Cfgs= 1
P: Vendor=1546 ProdID=01a7 Rev= 1.00
S: Manufacturer=u-blox AG - www.u-blox.com
S: Product=u-blox 7 - GPS/GNSS Receiver
C:* #Ifs= 2 Cfg#= 1 Atr=c0 MxPwr=100mA
I:* If#= 0 Alt= 0 #EPs= 1 Cls=02(comm.) Sub=02 Prot=01 Driver=cdc_acm
E: Ad=83(I) Atr=03(Int.) MxPS= 64 Ivl=255ms
I:* If#= 1 Alt= 0 #EPs= 2 Cls=0a(data ) Sub=00 Prot=ff Driver=cdc_acm
E: Ad=01(O) Atr=02(Bulk) MxPS= 64 Ivl=0ms
E: Ad=82(I) Atr=02(Bulk) MxPS= 64 Ivl=0ms
T: Bus=01 Lev=02 Prnt=02 Port=03 Cnt=02 Dev#= 3 Spd=480 MxCh= 0
D: Ver= 2.01 Cls=00(>ifc ) Sub=00 Prot=00 MxPS=64 #Cfgs= 1
P: Vendor=0424 ProdID=4940 Rev= 1.30
S: Manufacturer=Microchip Tech
S: Product=USB2 Controller Hub
C:* #Ifs= 1 Cfg#= 1 Atr=c0 MxPwr= 0mA
I:* If#= 0 Alt= 0 #EPs= 0 Cls=ff(vend.) Sub=ff Prot=ff Driver=(none)
127|root@jacinto6evm:/ # cat /dev/ttyACM0
$GPTXT,01,01,02,u-blox ag - www.u-blox.com*50
$GPTXT,01,01,02,HW UBX-G70xx 00070000 FF7FFFFFo*69
$GPTXT,01,01,02,ROM CORE 1.00 (59842) Jun 27 2012 17:43:52*59
$GPTXT,01,01,02,PROTVER 14.00*1E
$GPTXT,01,01,02,ANTSUPERV=AC SD PDoS SR*20
$GPTXT,01,01,02,ANTSTATUS=OK*3B
$GPTXT,01,01,02,LLC FFFFFFFF-FFFFFFFF-FFFFFFFF-FFFFFFFF-FFFFFFFD*2C
$GPRMC,201427.00,A,5542.94581,N,03747.44747,E,0.471,,090822,,,A*75
$GPVTG,,T,,M,0.471,N,0.872,K,A*2C
$GPGGA,201427.00,5542.94581,N,03747.44747,E,1,08,1.37,223.1,M,13.1,M,,*56
$GPGSA,A,3,30,13,07,14,05,08,15,27,,,,,2.36,1.37,1.93*04
$GPGSV,3,1,12,05,27,252,26,07,37,094,31,08,27,050,14,13,58,287,26*7E
$GPGSV,3,2,12,14,65,180,22,15,27,306,25,17,07,157,16,18,00,316,*7F
$GPGSV,3,3,12,20,07,223,,23,04,345,,27,05,020,13,30,70,100,31*7C
$GPGLL,5542.94581,N,03747.44747,E,201427.00,A,A*6F
$GPTXT,01,01,01,NMEA unknown msg*58
$GPRMC,201428.00,A,5542.94577,N,03747.44751,E,0.378,,090822,,,A*7A
$GPVTG,,T,,M,0.378,N,0.699,K,A*29
$GPGGA,201428.00,5542.94577,N,03747.44751,E,1,08,1.36,223.2,M,13.1,M,,*55
$GPGSA,A,3,30,13,07,14,05,08,15,27,,,,,2.36,1.36,1.92*04
$GPGSV,3,1,12,05,27,252,25,07,37,094,31,08,27,050,12,13,58,287,26*7B
$GPGSV,3,2,12,14,65,180,21,15,27,306,25,17,07,157,16,18,00,316,*7C
$GPGSV,3,3,12,20,07,223,,23,04,345,,27,05,020,13,30,70,100,31*7C
$GPGLL,5542.94577,N,03747.44751,E,201428.00,A,A*6E
^C