The reason for the funny behaviour is the use of CC64 Sustain data for a specific Channel in a previous Seq file which remains affecting that Channel until the appropriate CC code is sent. For example: If CC64 Sustain is used to enhance a Piano track on Channel2 and then a new Seq file loaded with Channel 2 used for a string patch then distortion will be experienced as chords are changed before the previous sustained chords have finished.

You can use the Sysex to reset the Synth or Mac's solution which is the quickest. Because I prefer to add a couple of extra Controller and one RPN (Registered Parameter Number) codes to each track, I have a Seq file with the first 16 tracks - Channels 1 to 16 containing the Controller data. This Seq file can then be opened via the File > Load Scrap and Pasted - Merge with existing data into the first 16 tracks of your song.