Force Sync

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I have a few .flv files that I want to convert to .mp4, but when I did so, the audio and video became severely out of sync using Format Factory. I have one ripper that has a force sync function, but I can't use it, because it only works encoding from a DVD.

That leaves the question of whether there is a free converter available that does have a force sync feature that works on a local file?
 

My Computer

Computer Manufacturer/Model Number
DIY
OS
W7x64 Pro, SuSe 12.1/** W7 x64 Pro, XP MCE
CPU
Phenom II 1090T w/Noctua NH-D14 /**4400+ X2 w/CM Hyper TX 3
Motherboard
ASRock 890FX Deluxe 4/**A8N-SLI
Memory
2 x 2GB Patriot PGS34g1600LLKA/**4x1GB Corsair VS
Graphics Card(s)
EVGA GTX460 SC/**EVGA 8800GTS
Sound Card
Asus Xonar D2X/**Xonar D1
Monitor(s) Displays
Acer X233H, Dell E152FPc /**LG M237-WD
Screen Resolution
1920x1080 & 1024x768/**1980x1080
Hard Drives
WDC 2TB, 1.5TB, 1TB, 500GB,Seagate 500GB , Maxtor 80GB /**500GB Seagate & WDC 1TB Black
PSU
CM RS600 w/ APC BX1000G/**Antec 500 TP w/ APC BX1000
Case
HAF922/**Antec 1040IIB
Cooling
3x200mm, 1x140 and 1x120mm/**5x80mm fans
Keyboard
Logitech Media USB/**Saitek Eclipse
Mouse
Cordless Trackman Wheel/**Ditto
Internet Speed
3.3Mbps
Other Info
SB 560 5.1 w/ Sennheiser RS140/**Creative T20 speakers, Dvico FusionHDTV7 Gold RT, Cisco E3000, HP 5510V AIO, Linksys E3000, Belkin F5U237 hub and **F5D8055 adapter
(** = 2nd rig)

My Computer

Computer type
PC/Desktop
Computer Manufacturer/Model Number
Apple 2012 Mac Mini
OS
Mac OS X 10.9
CPU
Intel i7 Ivy Bridge (2.3Ghz)
Motherboard
Apple
Memory
8GB's DDR3 (1333 MHz)
Graphics Card(s)
Intel 4000 (1024MB)
Monitor(s) Displays
HP 23inch LED
Screen Resolution
1920 x 1080
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1TB
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Mac Mini Case
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Mac Logitech Solar Powered
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Magic Touch Pad
Internet Speed
About 3.00 MBps
Browser
Chrome
It took some tinkering, but I finally got an conversion that is much improved over what I had, using Any Video. The first time around was even worse than with Format Factory, but changing the audio sync from basic to default synced the A/V to where the sync factor is only a split second apart. If that is as good as it is going to get, then so be it, but I really would like to perfect the sync...if possible.
 

My Computer

Computer Manufacturer/Model Number
DIY
OS
W7x64 Pro, SuSe 12.1/** W7 x64 Pro, XP MCE
CPU
Phenom II 1090T w/Noctua NH-D14 /**4400+ X2 w/CM Hyper TX 3
Motherboard
ASRock 890FX Deluxe 4/**A8N-SLI
Memory
2 x 2GB Patriot PGS34g1600LLKA/**4x1GB Corsair VS
Graphics Card(s)
EVGA GTX460 SC/**EVGA 8800GTS
Sound Card
Asus Xonar D2X/**Xonar D1
Monitor(s) Displays
Acer X233H, Dell E152FPc /**LG M237-WD
Screen Resolution
1920x1080 & 1024x768/**1980x1080
Hard Drives
WDC 2TB, 1.5TB, 1TB, 500GB,Seagate 500GB , Maxtor 80GB /**500GB Seagate & WDC 1TB Black
PSU
CM RS600 w/ APC BX1000G/**Antec 500 TP w/ APC BX1000
Case
HAF922/**Antec 1040IIB
Cooling
3x200mm, 1x140 and 1x120mm/**5x80mm fans
Keyboard
Logitech Media USB/**Saitek Eclipse
Mouse
Cordless Trackman Wheel/**Ditto
Internet Speed
3.3Mbps
Other Info
SB 560 5.1 w/ Sennheiser RS140/**Creative T20 speakers, Dvico FusionHDTV7 Gold RT, Cisco E3000, HP 5510V AIO, Linksys E3000, Belkin F5U237 hub and **F5D8055 adapter
(** = 2nd rig)
I get a video sync issue on about one in five videos that I convert with Format factory.
 

My Computer

Computer Manufacturer/Model Number
Custom Built
OS
Windows 7 Professional 64bit
CPU
Dual Xenon X5272 3.4Ghz
Motherboard
Tyan S5397
Memory
Kingston 16 Gig PC6400 (4 DIMMs)
Graphics Card(s)
Nvidia GTX 280
Sound Card
Soundblaster X-Fi Fatal1ty
Monitor(s) Displays
Samsung SyncMaster 24
Screen Resolution
1920 x 1200
Hard Drives
LSI - 4 SAS 15K in Raid 0
Adaptec - 4 SAS 15K in Raid 0
Cooling
Water Cooled
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