1.4.3 and 2.0 use the same sites.dat format. Unless there is some corruption in your sites.dat file I can't think of any other explanation for this type of problem.
If you can email me your sites.dat at
support@flashfxp.com I will examine it and see if the problem is with FlashFXP or the sites.dat and making any repairs if possible.
Alternatively you may have to re-enter all of your sites.