Geany 1.29 "Jowar" compiled 2016-07-16 / Windows 7-64 Bit
and also
Geany 1.29 "Jowar" compiled 2016-09-08 / Windows 7-64 Bit

If you select -> Lineend will be
Set to CR -> 0x0d
Set to LF -> 0x0d 0x0a
Set to CR/LF -> 0x0d 0x0d 0x0a

Except with "Set to CR" there is an additional 0x0d.

SciTE 3.6.7 / Windows 7-64 Bit does it right.
Geany Release 1.28 / Windows 7-64 Bit does it right.

The problem seems to be connected with the recognition of the lineend when opening a file.
With Geany 1.28 when I open a file with CR/LF as lineend then "Document/Set Lineend/Set to CR/LF and convert" is preselected.
When I open this file with Geany 1.29 then "Document/Set Lineend/Set to LF and convert" is preselected.

I attached three small test files with lineend CR, CR/LF and LF for convenience.

test_cr.txt
test_crlf.txt
test_lf.txt

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