Do as Recap said and install 640x484 or 648x480 (whatever that's not exactly 640x480), then use that new mode for the desktop. Try launching those emulators after doing this.
Thank you for the help! I attempted once more with Recap & your suggestion but still am losing sync. Here is what my .ini file looks like:
## Desktop ##
640 x 484 @ 60.000000 desktop
## Redream ##
640 x 240 @ 60.000000 redream
720 x 480 @ 59.940000 redream
## Super resolutions ##
320 x 240 @ 60.000000 super
2560 x 240 @ 60.000000 super
2560 x 248 @ 60.000000 super
2560 x 256 @ 60.000000 super
2560 x 264 @ 60.000000 super
2560 x 272 @ 60.000000 super
2560 x 280 @ 60.000000 super
2560 x 288 @ 60.000000 super
2560 x 296 @ 60.000000 super
2560 x 304 @ 60.000000 super
2560 x 320 @ 60.000000 super
2560 x 336 @ 60.000000 super
2560 x 344 @ 60.000000 super
2560 x 352 @ 60.000000 super
2560 x 360 @ 60.000000 super
2560 x 368 @ 60.000000 super
2560 x 376 @ 60.000000 super
2560 x 384 @ 60.000000 super
2560 x 392 @ 60.000000 super
2560 x 400 @ 60.000000 super
2560 x 416 @ 60.000000 super
2560 x 432 @ 60.000000 super
2560 x 448 @ 60.000000 super
2560 x 464 @ 60.000000 super
2560 x 480 @ 60.000000 super
2560 x 496 @ 60.000000 super
2560 x 512 @ 59.000000 super
2560 x 544 @ 55.000000 super
2560 x 560 @ 54.000000 super
2560 x 768 @ 60.000000 super
2560 x 800 @ 60.000000 super
2560 x 192 @ 60.000000 retroarch
2560 x 200 @ 60.000000 retroarch
2560 x 240 @ 60.000000 retroarch
2560 x 224 @ 60.000000 retroarch
2560 x 237 @ 60.000000 retroarch
2560 x 256 @ 50.000000 retroarch
2560 x 254 @ 55.000000 retroarch
2560 x 448 @ 60.000000 retroarch
2560 x 480 @ 60.000000 retroarch
320 x 240 @ 60.000000 retroarch
720 x 480 @ 59.940000 retroarch
720 x 480 @ 60.000000 retroarch
And here is what VMM says it's installed:
"320x240_60 15.66KHz 60.00Hz" 6.64 320 336 368 424 240 242 245 261 -hsync -vsync
"640x240_60 15.66KHz 60.00Hz" 13.03 640 664 728 832 240 242 245 261 -hsync -vsync
"640x484_60 15.75KHz 60.00Hz" 13.10 640 664 728 832 484 486 492 525 interlace -hsync -vsync
"720x480_60 15.69KHz 60.00Hz" 14.81 720 752 824 944 480 483 489 523 interlace -hsync -vsync
"2560x192_60 15.66KHz 60.00Hz" 52.12 2560 2664 2912 3328 192 218 221 261 -hsync -vsync
"2560x200_60 15.66KHz 60.00Hz" 52.12 2560 2664 2912 3328 200 222 225 261 -hsync -vsync
"2560x224_60 15.66KHz 60.00Hz" 52.12 2560 2664 2912 3328 224 234 237 261 -hsync -vsync
"2560x237_60 15.66KHz 60.00Hz" 52.12 2560 2664 2912 3328 237 240 243 261 -hsync -vsync
"2560x240_60 15.66KHz 60.00Hz" 52.12 2560 2664 2912 3328 240 242 245 261 -hsync -vsync
"2560x248_60 16.14KHz 60.00Hz" 54.23 2560 2672 2928 3360 248 250 253 269 -hsync -vsync
"2560x254_59 16.20KHz 58.91Hz" 54.43 2560 2672 2928 3360 254 256 259 275 -hsync -vsync
"2560x256_58 16.20KHz 58.48Hz" 54.43 2560 2672 2928 3360 256 258 261 277 -hsync -vsync
"2560x264_57 16.20KHz 56.84Hz" 54.43 2560 2672 2928 3360 264 266 269 285 -hsync -vsync
"2560x272_55 16.20KHz 55.29Hz" 54.43 2560 2672 2928 3360 272 274 277 293 -hsync -vsync
"2560x280_54 16.20KHz 53.82Hz" 54.43 2560 2672 2928 3360 280 282 285 301 -hsync -vsync
"2560x288_52 16.20KHz 52.43Hz" 54.43 2560 2672 2928 3360 288 290 293 309 -hsync -vsync
"2560x448_60 15.69KHz 60.00Hz" 52.22 2560 2664 2912 3328 448 467 473 523 interlace -hsync -vsync
"2560x464_60 15.69KHz 60.00Hz" 52.22 2560 2664 2912 3328 464 475 481 523 interlace -hsync -vsync
"2560x480_60 15.69KHz 60.00Hz" 52.22 2560 2664 2912 3328 480 483 489 523 interlace -hsync -vsync
"2560x496_60 16.17KHz 60.00Hz" 54.33 2560 2672 2928 3360 496 499 505 539 interlace -hsync -vsync
"2560x512_58 16.23KHz 58.48Hz" 54.66 2560 2672 2928 3368 512 515 521 555 interlace -hsync -vsync
"2560x544_55 16.23KHz 55.29Hz" 54.65 2560 2672 2928 3368 544 547 553 587 interlace -hsync -vsync
"2560x560_54 16.23KHz 53.82Hz" 54.65 2560 2672 2928 3368 560 563 569 603 interlace -hsync -vsync
>>modelist install
Installing modelines in system...
23 modelines installed.
Does it have something to do with some of them saying interlaced and some not?
Thanks again for the help!