Why are identical words pronounced differently at certain locations of the Shema?

Question

Why are identical words pronounced differently at certain locations of the Shema? Or is this only for Sefardim? The two identical phrases in question are in the Veahávta and then again in the Vehayá:

1. "beshivtéja beveitéja uvlejtéja vadérej, uvshojbéja uvkuméja." (Please note the change of accent mark between both readings)
2. "beshivtejá beveitéja, uvlejtejá vadérej uvshojbejá uvkuméja. (The J should be read as CH for Ashkenazim)

Keep in mind that I'm not referring to differences between Sefardim vs Ashkenazim pronunciation, but within the Shema itself. I will assume that this pronunciation may apply to Ashkenazim as well and that the issue may be one of Hebrew grammar. But what exactly is that rule (if it is one of grammar)?

The example above was taken from the Sidur Tefilát Binyamin by Benjamin Senker

Answer 1

The two passages are from Deuteronomy 6:7 and 11:19, respectively:

1. וְשִׁנַּנְתָּ֣ם לְבָנֶ֔יךָ וְדִבַּרְתָּ֖ בָּ֑ם בְּשִׁבְתְּךָ֤ בְּבֵיתֶ֙ךָ֙ וּבְלֶכְתְּךָ֣ בַדֶּ֔רֶךְ וּֽבְשָׁכְבְּךָ֖ וּבְקוּמֶֽךָ׃

2. וְלִמַּדְתֶּ֥ם אֹתָ֛ם אֶת־בְּנֵיכֶ֖ם לְדַבֵּ֣ר בָּ֑ם בְּשִׁבְתְּךָ֤ בְּבֵיתֶ֙ךָ֙ וּבְלֶכְתְּךָ֣ בַדֶּ֔רֶךְ וּֽבְשָׁכְבְּךָ֖ וּבְקוּמֶֽךָ׃

Note that both the vowels and the cantillation marks - which denote accentation - on these words are identical in the Torah. I've never heard of any dispute in tradition about either of these elements of these verses. The accent marks in your transliteration of (1) are incorrect and should be corrected to match those of (2).