I have had a similar instance where repeatedly pressing the align key (B) makes SEVERAL adjustments, until it settles on what it believes is "aligned".
I have also had some issues with different fonts aligning a "relative" baseline, as opposed to an "actual" baseline. For example, anything with a "tail" that hangs below the baseline (i.e. lowercase y, p, q,j etc) will sometimes align the bottom of the letter with the baseline of the other word - which can be an issue if the other word has no letters with "tails". So instead of getting all of the letters to sit on the same line, and having the appropriate tails hanging below the line, the word with tails sits above the base line, while the tip of the tail touches the baseline. This may be the phenomenon you are experiencing. In some instances the multiple pressing of the align button helps, other times I have to align the centers or the tops of the word. The final option is to use the dynamic guidelines and start the guideline on the base of the first word, drag it out to the position where the second word is supposed to begin, and then begin typing. Insuring snap to guidelines is on helps.