Did you go to the Cockpit (the default keyboard shortcut is F10) to initialize it? Or did you move the initialisation line to [VCockpit01], which initialises the CIVA INS as soon as the 707 loads into FSX/FSX-SE (see bellow)?

Move the gauge04=../civa/INS!Config,         0,    0,  0, 0, csx701:

[Window00]
file=bg.bmp
background_color=0,0,0
size_mm=1024,768
window_size_ratio=1.00   
position=7
visible=1
ident=MAIN_PANEL
render_3d_window=0
window_size= 1.000, 1.000
window_pos= 0.000, 0.000
gauge00=Captain_Sim.x707.sys!main, 0,0, 2,2
gauge01=Captain_Sim.x707.sound!main, 0,0,1,1,Captain_Sim\707\sound.ini
gauge02=Captain_Sim.x707.tools!icons, 0,532,24,120
gauge03=Captain_Sim.x707.gpws!main, 0,0,1,1
;CIVA
gauge04=../civa/INS!Config,         0,    0,  0, 0, csx701
gauge05=../civa/INS!NavModeSingle,  0,  652,  1, 1        (then change this to gauge04= etc.)
gauge06=../civa/INS!CduPanelIcon,   0,  652, 24, 24, 11041        (then change this to gauge05= etc.)
gauge07=../civa/INS!MsuPanelIcon,   0,  676, 24, 24, 11040        (then change this to gauge06= etc.)
gauge08=../civa/INS!AdeuPanelIcon,  0,  700, 24, 24, 11042        (then change this to gauge07= etc.)

To here:

[VCockpit01]
size_mm=1024,1024
pixel_size=1024,1024
texture=$FPSP
background_color=0,0,0
gauge00=Captain_Sim.x707.R01!R01_001_light, 625, 824, 56,55
gauge01=Captain_Sim.x707.R02!R02_clock, 50, 300, 155,151
gauge02=Captain_Sim.x707.R03!R03_aplight, 625, 750, 55,55
gauge03=Captain_Sim.x707.R05!R05_rmi, 275, 775, 200,200
gauge04=Captain_Sim.x707.R06!R06_001_light, 500,450, 58,57
gauge05=Captain_Sim.x707.R06!R06_002_light, 498,526, 58,57
gauge06=Captain_Sim.x707.R06!R06_003_light, 502,854, 58,57
gauge07=Captain_Sim.x707.R06!R06_004_light, 502,925, 60,57
gauge08=Captain_Sim.x707.R08!R08_hsi, 602, 275, 375, 374      
gauge09=Captain_Sim.x707.R09!R09_001_light, 402,126, 57,57
gauge10=Captain_Sim.x707.R09!R09_002_light, 402,202, 57,57
gauge11=Captain_Sim.x707.R10!R10_altimeter, 280,280, 190,214
gauge12=Captain_Sim.x707.R11!R11_vsi, 725,700, 289,289
gauge13=Captain_Sim.x707.R13!R13_ra, 252,499, 254,254
gauge14=Captain_Sim.x707.R13!R13_001_light, 500,675, 50,50
gauge15=Captain_Sim.x707.R14!R14_001_light, 300,0, 76,75
gauge16=Captain_Sim.x707.R17!R17_008_ndl, 500,125, 130,130
gauge17=Captain_Sim.x707.R17!R17_001_light, 0,0,   75,75
gauge18=Captain_Sim.x707.R17!R17_002_light, 75,0,  75,75
gauge19=Captain_Sim.x707.R17!R17_003_light, 150,0, 75,75
gauge20=Captain_Sim.x707.R17!R17_004_light, 225,0, 75,75
gauge21=Captain_Sim.x707.R18!R18_001_light, 925,25, 75,75
gauge22=Captain_Sim.x707.R18!R18_002_light, 925,100, 75,75
gauge23=Captain_Sim.x707.R18!R18_003_light, 925,175, 75,75
gauge24=Captain_Sim.x707.R16!R16_3D, 25,525,230,74
gauge25=Captain_Sim.x707.menu!main, 0, 0, 1, 1
gauge26=Captain_Sim.x707.sound!main, 0,0,1,1,Captain_Sim\707\sound.ini
;CIVA
gauge27=../civa/INS!Config,         0,    0,  0, 0, csx701

The csx701.Isd file should be in the FSX\Civa folder. If it isn't there, then the CIVA INS hasn't initialsed the INS for the 707 yet.