Recombination frequency, linked genes, and independent assortment
The comments pretty much answer the main concern here. But just to sum up:-  


  "....T and X assort independently, so they should be on different
  chromosome...." 


Not necessarily. They can be on the same chromosome at such a distance that there is usually atleast one chiasma formation between them, and will undergo independent assortment, i.e.  segregation of one gene among the gametes will be independent of the other. They will pretty much act and segregate like mendelian factors. Specifically, if the recombination frequency is 0.5 (50cM or map units' distance on the chromosome), they will assort independently.  


  "....And then due to recombination, X gene crosses over so that it's also
  on the same chromosome as T and R...."  


This part is a little bit unclear. I assume (correct me if I am wrong) is that you are assuming X,T,R to be alleles, which can be present on only one chromatid and hence recombination might change their distribution and positions relative to one another. But as the question states, they are genes (or specifically gene loci) which are present on both chromatids and their relative position is fixed. The recombination frequencies refer to the recombination of different alleles at this locus.