There are 2 possible solutions :
1- Use the installation command line :
Example for CU5 agent patch (99111570) :
DeployWrapper.exe /INST ApplyPtfInstall /PTF=99111570.jcl /SILENT /INSTALLNEW /OUTPUTFILE=99111570.log
or
APPLYPTF.exe /NODE=computername /PTF=99111570.jcl /SILENT /INSTALLNEW /OUTPUTFILE=99111570.log
change computername by the correct hostname
OR
2- With applyptf.exe in interactive mode :
Edit file 99111570.jcl and replace the lines
FILE:#TNGDTS-30#\bin\dtscli.exe:SKIPIFNOTFOUND:
FILE:#TNGDTS-30#\bin\dtscore11.dll:SKIPIFNOTFOUND:
FILE:#EGC30N#\EGC30N.dll:SKIPIFNOTFOUND:
FILE:#TNGDTS-30#\bin\tngdta.exe:SKIPIFNOTFOUND:
FILE:#TNGDTS-30#\bin\dtfzlib.dll:SKIPIFNOTFOUND:
by these lines :
FILE:..\SC\DTS\bin\dtscli.exe:SKIPIFNOTFOUND:
FILE:..\SC\DTS\bin\dtscore11.dll:SKIPIFNOTFOUND:
FILE:..\SC\EGC\EGC30N.dll:SKIPIFNOTFOUND:
FILE:..\SC\DTS\bin\tngdta.exe:SKIPIFNOTFOUND:
FILE:..\SC\DTS\bin\dtfzlib.dll:SKIPIFNOTFOUND:
This second solution does not work if DTS agent and/or DSM Explorer are installed on the Agent/Server machine but with a different path than DSM.
Example :
DSM installed under C:\Program Files (x86)\CA\DSM
SC installed under D:\Program Files (x86)\CA\SC