You have to type nameoffile.mid (And you need to add .mid), then put nameofsseq.sseq (You must add .sseq). To use it, you must point a Command Prompt window to the location of it, but it seems you've done that already as you're seeing that message.
Example:
C:\Users\YourName\Documents\midi2sseq input.mid output.sseq
C:\<location on your hard drive>\midi2sseq input.mid output.sseq
Yeah, it already had both extensions and it gave me this:
C:\Documents and Settings\User Folder\midi2sseq input.mid output.sseq
Usage:
midi2sseq midifile sseqfile
But now it's being crazy and giving me this:
C:\Documents and Settings\User Folder\midi2sseq input.mid output.sseq
Warning: note on on active note! Track 13, pos 99
Warning: note off on non-existant note! Track 13, pos 102
Warning: note on on active note! Track 3, pos 173
Warning: note off on non-existant note! Track 3, pos 176
Warning: note on on active note! Track 3, pos 179
Warning: note off on non-existant note! Track 3, pos 182
Warning: note on on active note! Track 3, pos 185
Warning: note off on non-existant note! Track 3, pos 188
Warning: note on on active note! Track 3, pos 191
Warning: note off on non-existant note! Track 3, pos 194
Warning: note on on active note! Track 3, pos 197
Warning: note off on non-existant note! Track 3, pos 200
Warning: note on on active note! Track 3, pos 203
Warning: note off on non-existant note! Track 3, pos 206
Warning: note on on active note! Track 3, pos 209
Warning: note off on non-existant note! Track 3, pos 212
Warning: note on on active note! Track 3, pos 215
Warning: note off on non-existant note! Track 3, pos 218
Warning: note on on active note! Track 3, pos 221
Warning: note off on non-existant note! Track 3, pos 224
Warning: note on on active note! Track 3, pos 227
Warning: note off on non-existant note! Track 3, pos 230
Warning: note on on active note! Track 3, pos 233
Warning: note off on non-existant note! Track 3, pos 236
Warning: note on on active note! Track 3, pos 239
Warning: note off on non-existant note! Track 3, pos 242
Warning: note on on active note! Track 3, pos 245
Warning: note off on non-existant note! Track 3, pos 258
Warning: note on on active note! Track 3, pos 251
Warning: note off on non-existant note! Track 3, pos 254
Warning: note on on active note! Track 3, pos 257
Warning: note off on non-existant note! Track 3, pos 260
Warning: note on on active note! Track 3, pos 263
Warning: note off on non-existant note! Track 3, pos 267
Warning: note on on active note! Track 3, pos 272
Warning: note off on non-existant note! Track 3, pos 276
Warning: note on on active note! Track 3, pos 279
Warning: note off on non-existant note! Track 3, pos 284
Warning: note on on active note! Track 3, pos 287
Warning: note off on non-existant note! Track 3, pos 292
Warning: note on on active note! Track 3, pos 295
Warning: note off on non-existant note! Track 3, pos 300
Warning: note on on active note! Track 3, pos 303
Warning: note off on non-existant note! Track 3, pos 308
Warning: note on on active note! Track 3, pos 315
Warning: note on on active note! Track 3, pos 316
Warning: note off on non-existant note! Track 3, pos 321
Warning: note off on non-existant note! Track 3, pos 322
Warning: note on on active note! Track 3, pos 325
Warning: note off on non-existant note! Track 3, pos 330
Warning: note on on active note! Track 3, pos 333
Warning: note on on active note! Track 3, pos 334
Warning: note off on non-existant note! Track 3, pos 339
Warning: note off on non-existant note! Track 3, pos 340
Warning: note on on active note! Track 3, pos 343
Warning: note off on non-existant note! Track 3, pos 348
Warning: note on on active note! Track 3, pos 351
Warning: note off on non-existant note! Track 3, pos 356
Warning: note on on active note! Track 3, pos 359
Warning: note off on non-existant note! Track 3, pos 364
By any chance, is this even supposed to happen?