I believe that Suse Yast2 selects the modem kernel driver settings from the modem module.
Let's try two things:
1) Try it manually:
root@linux:/# wvdial -C /etc/wvdial.conf
root@linux:/# ifconfig ppp0

A similar output should be displayed:
ppp0
Link encap:Point-to-Point Protocol
inet addr:10.69.60.203 P-t-P:192.168.254.254 Mask:255.255.255.255
UP POINTOPOINT RUNNING NOARP MULTICAST MTU:1500 Metric:1
RX packets:4 errors:0 dropped:0 overruns:0 frame:0
TX packets:5 errors:0 dropped:0 overruns:0 carrier:0
collisions:0 txqueuelen:3
RX bytes:64 (64.0 b) TX bytes:97 (97.0 b)
Does that look like what you manually designated?
Alternate Solution: You can start your modem automatically and bypass Yast2 by adding your startup string directly to /etc/rc.local at boot:
/usr/sbin/wvdial -C /etc/wvdial.conf
[make sure that's the correct path]
2) Verify your settings in Yast2

Yast modem configuration documentation:
In the YaST Control Center, access the modem configuration with Network Devices > Modem. If your modem was not automatically detected, open the dialog for manual configuration by clicking Add. In the dialog that opens, enter the interface to which the modem is connected for Modem Device.

Configure supported CDMA and GPRS modems with the YaST modem module just as you would configure regular modems.

From: http://www.novell.com/documentation/sles10/sles_admin/index.html?page=/documentation/sles10/sles_admin/data/sec_basicnet_yast.html
It's a fairly good bet that your settings are being passed to the modem, but the kernel driver and modem itself is not compatible with those settings.
You say that these were the same in XP? I am not understanding... Did you recently rebuild this server? Are you running a liveCd or comparing the modem as initialized in another computer?
Also, what is your process to compare your download and throughput time, just out of curiosity?

BUT THE BIG QUESTION is whether this is a WINMODEM or not? It's always worth doing a quick two page google of:
1) Your MODEM device manufacturer and model.
2) Your distro version.
3) Any error - in this case MTU..

Some modems have specific anomolies based on known hardware limitations of the specification, kernel driver issues, and distro (just like ethernet, graphics cards, etc).

Use the Source, young Jedi!
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> Date: Sat, 20 Dec 2008 14:58:00 -0700
> From: mzyniecki@gmail.com
> To: plug-discuss@lists.plug.phoenix.az.us
> Subject: Re: newbie has problems w/ dialup
>
> Based on the suggestions and some research, I've modified the MTU and
> MRU to appropriate values for dialup. In /etc/ppp/options I've added
> two lines after the line "crtstcs":
> MTU 576
> MRU 512
>
> When the modem is connected /sbin/ifconfig shows the following for modem0:
> UP POINTOPOINT RUNNING NOARP MULTICAST MTU:512 Metric:1
> There is still no overall difference in download speed. Still takes
> 170-180 seconds to download 150 Kb.
>
> It seemed worth it to try changing from the openSUSE to the WinXP init
> string since the differences in the Hayes commands don't seem that
> significant (although I wonder why echo is on in openSUSE and off in
> WinXP.). YaST2 recognizes the modem (/dev/ttyUSB0). However, I can't
> get it to maintain changes after clicking all the way through to
> "finish". Each time I return through YaST the modem baud rate is back
> to the highest rate (400000) instead of the 57600 I changed it to, and
> the init string is back to the openSUSE original from the WinXP
> substitution.
>
> Sooo, I modified /etc/wvdial.conf. Changed baud to 57600 and the init
> string to the WinXP version. After connecting to the Internet, I
> examined the KInternet log, which showed wvdial used the openSUSE init
> string instead of the WinXP version substituted in wvdial.conf.
> Checking wvdial.conf, the substitutions were there, and checking
> through YaST, the baud was back to 4000000 and the openSUSE init
> string was back.
>
> QUESTIONS:
> 1.) Why does ifconfig show MTU 512 when /etc/ppp/options has MTU 576?
> 2.) How do I get YaST to accept the baud rate and init string changes
> or get wvdial.conf to execute the changes?
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