Using 6.04.01, I created a druid with a wolf animal companion. Checked companion size and confirmed as Medium.
Leveled character to 3rd, checked companion level again, size reverted to small.
Checked the rsrd_companionmods.lst file for the entry on wolf. Found a previous work around that addressed an earlier issue with companions increasing size at level 3. (from DATA-1654) I commented out the line for wolf and it appeared to correct the sizing issue.
I then tested in the same manner in 6.05.03 and found the same issue.
It appears that the previous sizing issue was corrected somewhere else, but the lst file was never updated to reflect the fixes.
Win 7 pro,