So, I was just testing mkototemp to see what it might be, and the only solution I could find was to add literally any single character to the start of every line. I'm not sure why, but it seems to expect that there will be an unused character at the start of every line (probably due to the common practice of starting lines with underscores). So if you put an underscore at the beginning of every line, it will ignore the underscore and properly read the lines instead of ignoring the first kana since it seems to be programmed to ignore the first character of every line regardless of what it is.
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If you don't want to deal with adding the underscores in the reclist, my next best suggestion would be to take what it gives you and just manually add in the missing lines as you go. If the reclist isn't many lines, I'd just add the underscores, but if its a lot of lines and it would be too tedious to add underscores to every line, I'd probably just add the missing lines as I oto.
