edit: After a quick search, both pronunciations are given. In fact, my IME immediately gave me the correct kanji for いっぱこ but not for ひとはこ.
OMG, MS-IME(I assume you use this, right?) does it again! (again and again and again?

)
Please do NOT put too much trust in MS-IME. 一箱 is commonly pronounced as ひとはこ, not いっぱこ. (JFYI,
ATOK can convert ひとはこ to 一箱 correctly...)
Basically, いち(いっ), に, さん,,, is used with 漢語/音読み, and ひと, ふた, み,,, is used with 和語/訓読み.
e.g.
一通、二通、三通; いっつう、につう、さんつう
一通り、二通り、三通り; ひととおり、ふたとおり、みとおり/さんとおり(basically みとおり, but さんとおり is also acceptable recently.)
一間、二間、三間; いっけん、にけん、さんげん/さんけん
*This 間 is a unit to measure length. 一間 equalls about 180cm.
一間、二間、三間; ひとま、ふたま、みま
*This 間 is a counter used for counting number of rooms. (この家には和室が二間ある。)