hi. dose your plasmid contain a transmissible  elements thus the desire gene transfer from plasmid to chromosome ? or may be your parasite just adapted  for the character and after few generation the trail will be lost 

There are several factors that could be causing this result.  The P. falciparum Dd2 could  be resistant to the drugs being used, or drug concentrations could be too low. Long DNA fragments have been found to be unstable in E. Coli, which could prove fatal for the transformed cells.  The transformation process could be killing the E. coli as well.  For real help, more information would be required about your methods.