In the above example, I didn't have to use the "align" functions because I entered each line of text in one shot. In other words, I didn't stop lyric entry (by hitting return) and then resume again. But as you know, if you do stop/resume and the alignment of the lyrics are off kilter as a result, select them and use Align Vertically.
The horizontal alignment also fell nicely into place too and didn't require any additional editing. However, while messing around to see if I could replicate the behavior you described, I was reminded that there is an alignment parameter for lyrics. See the attached screenshot as to which one I think you should have selected.
I'd say this... if you continue having trouble with lyric entry, by far the easiest way to make things right would be to type them over and "follow the protocol" of lyric entry to the letter (no pun intended). Here it is:
1) turn guides on (this will be super helpful!!)
2) select the lyric item in the partbox, select the pencil tool, and click under the first note
TROUBLESHOOTING STEP: at this point, hit return/enter to conclude lyric entry. Select that lyric (if not already selected) and click on that alignment thingy in the event parameters. Make sure it's set to what you see in the screenshot. If it's not, change it to what you see there. This should set that parameter for all additional lyrics you enter. Then resume lyric entry:
3) with the lyric item selected in the partbox, choose the pencil tool & click under the next note
4) type the lyric and TAB to the next note. Type, TAB, type, TAB. If you need to skip a note, just hit TAB to move on to the next note.
5) conclude lyric entry with Return or Enter
6) resume lyric entry as needed from Step 3
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