It appears that you are correct about the village name, though without being able to view the original records directly so that we can use our own photo editing programs to enlarge, sharpen and otherwise modify the images, it difficult to be sure. Perhaps if you gave enough information so that we could examine the records ourselves, we could be more helpful.
There are 3 villages named Kaniukai near Alytus. The way that Poles or Russians spell the name would be the same no matter which village is referenced, just as the way any name would be spelled by any ethnic group -- assuming a reasonable degree of linguistic standardization. Lithuanian was only standardized after WWI and ethnic Lithuanians often used Polish spellings, especially prior to WWI when Polish was such a dominant influence there. Spellings found on manifests or other documents often vary significantly from one to another whatever the native language of the writer was.
You can see all 3 villages on this map:http://www.maps.lt/en
There are 39 listings for the surname Rac^kauskas in the Alytus area online phone book for Lithuania