The flv fixer in
GetFLV is just the same as (is actually lifted from) the freeware FLVMDI. So, it has all the same limitations as FLVMDI. It is mostly helpful for setting duration data, but it won't necessarily always start at 0:00.
The fix tool in
Jaksta is actually quite powerful, although I wish it had a few more options: like the ability to set the start hex value of the first time stamp, or the ability to do a range of timestamps without manual selection. But, it is very good for setting duration data and setting the timing interval values.
Some other tools to try are FLVTool2, and RichFLV. RichFLV requires adobe air, and often crashes while reading a file. But when it does work it does a good job.