that it is regarding **flatulence** and **sleeping**  

 [Tractate Shabbath 49A][1]

> R. Jannai said: Tefillin  demand a **pure body**, like Elisha, the man of wings. What does this mean? — Abaye said: That one must **not pass wind** while wearing them; Raba said: That one must **not sleep** in them.

sleeping is easy but flatulence is a problem

[shulchan aruch harav 28.5][2]

> the reason men do not wear teffilin all day is because they do not have a guf noki

and [36.2][3]

> not every man can be careful not to pass gas in them



the reason it is called guf noki maybe is because particles of feces getting suck to the body (http://judaism.stackexchange.com/questions/61866/)

i never saw that menstruation has to do with clean body




see [mogen avrochom 38.3][4] 

>מוחין כו'. מפני שצריכין גוף נקי ונשים אינם זריזות להזהר אבל אם היו חייבים לא היו פטורין מה"ט דהוי רמי אנפשייהו ומזדהרי כנ"ל דלא כע"ת:

where he says that it is because they are not careful to be watchful and that if they would have been obligated to wear them then this (not being careful of flatulence) will not be enough of a reason not to

but woman are anyway not obligated to wear them 

[Berakhot Chapter 3 mishna 3][5]
>Women, slaves, and minors are exempt from reciting Shema and from **Tefillin** ...

so better that they should not wear them, then maybe passing gas in them



ps (IMO this is since it is good for women not to be tense but relaxed (it is also better for the children))

i heard that their once was a time that even men stopped wearing teffilin since they where lazy from keeping their body clean (from passing gas), but [the rabbis were against this][6].


  [1]: http://halakhah.com/shabbath/shabbath_49.html
  [2]: http://chabadlibrary.org/books/adhaz/sh/sh1/5/28/5.htm
  [3]: http://chabadlibrary.org/books/adhaz/sh/sh1/5/37/2.htm
  [4]: http://beta.hebrewbooks.org/tursa.aspx?a=oc_x402
  [5]: http://www.sefaria.org/Mishnah_Berakhot.3.3?lang=en&layout=lines&sidebarLang=all
  [6]: http://chabadlibrary.org/books/adhaz/sh/sh1/5/37/1.htm