Hello.

First, would you please explain to me what you mean by "the document
does not get formatted correctly"? As in, does the embedding of the
Nimbus version of Times Roman result in changes in your workflow and end
result that it is unacceptable, and how so?

For your information, I can also reproduce your described situation on
at least one other TeX distro for the Win32 platform too. It is not
pdf(la)tex-specific either, as I can achieve the same embedded result
even using the latex, dvips and ps2pdf combination.

Also, say, suppose you load and use Helvetica fonts using the helvet
package, you will find that the embedded font is also a Nimbus version
(NimbusSans), and not Adobe Helvetica. So, your situation is not Times
Roman-specific either. The core set of Postscript Type 1 fonts that are
shipped with all up to date TeX distros are not the Adobe ones, but
versions donated by URW. So, no surprise that it is not the Adobe
versions that are embedded.

You mentioned that you upgraded from hoary to breezy to dapper, which
means you may have upgraded from teTeX 2 to teTeX 3. But whether this
upgrade is the cause of the problem cannot be determined unless you also
enable font embedding in teTeX 2 and check if you also get Nimbus
versions. In fact I think you will find that it is Nimbus, too.

To summarize, if font embedding is enabled, both the pdftex and dvips
compilation methods will embed Nimbus versions, because that is what
modern TeX distros are shipped with.

-- 
pdflatex not using correct fonts
https://launchpad.net/bugs/51508

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