There seems to be some inconsitency about the datum shift parameters for EPSG:5221.
Using gdalsrsinfo epsg:5221, GDAL 1.11.2 reports:
+proj=krovak +lat_0=49.5 +lon_0=42.5 +alpha=30.28813972222222 +k=0.9999 +x_0=0 +y_0=0 +ellps=bessel +towgs84=589,76,480,0,0,0,0 +pm=ferro +units=m +no_defs
Whereas the current QGIS 2.8.2 has this definition:
+proj=krovak +lat_0=49.5 +lon_0=42.5 +alpha=30.28813972222222 +k=0.9999 +x_0=0 +y_0=0 +ellps=bessel +towgs84=542.5,89.2,456.9,5.517,2.275,5.516,6.96 +pm=ferro +units=m +no_defs
towgs84 parameters are different (3-parms vs 7-parms). I'm not sure which one is more accurate, and if and when parameters changed in QGIS.
If you have still access to QGIS 2.0, look up the parameters there. You can set up a custom CRS in your running QGIS and assign it to the Krovak projected files.
Alternatively, you can save the WGS84 layer in QGIS 2.0 into Krovak projection, take it into QGIS 2.2, and save it back to WGS84 there. BTW, I suggest to update to QGIS 2.8.3. There are lots of bugs fixed since QGIS 2.2.
This bug report might be related: https://hub.qgis.org/issues/9760 and there was a patch in http://lists.osgeo.org/pipermail/qgis-commit/2013-June/010976.html. The quoted source for the parameters has moved to http://freegis.fsv.cvut.cz/gwiki/S-JTSK_/_%C4%8Ceskoslovensk%C3%BD_transforma%C4%8Dn%C3%AD_kl%C3%AD%C4%8D.
The site offers different shift parameters for the Czech Republic, Slovakia, and the whole former Czechoslovakia. The values now used by QGIS are for the last one, while GDAL still uses the 3-parms set up by NIMA when WGS84 was established.