Problem with encrypted ntfs partition?

On my laptop i have two disks - ssd and hdd. On the hdd i have encrypted ntfs partition with veracrypt under Windows. I am experience some slow performance on this partition: i have few virtalbox disks that start very slow, and also deleting files on that partition is slow. If i run 'fdisk -l' i see errors like this: 'Partition 1 does not start on physical sector boundary.' I am wondering what this errors mean and if this is not the reason for the slow performance i am experience on that partition?

Code:Disk /dev/sda: 111.8 GiB, 120034123776 bytes, 234441648 sectors
Disk model: KINGSTON SA400S3
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0xfa195d4a

Device Boot Start End Sectors Size Id Type
/dev/sda1 * 2048 104447 102400 50M 7 HPFS/NTFS/exFAT
/dev/sda2 104448 101363828 101259381 48.3G 7 HPFS/NTFS/exFAT
/dev/sda3 101365760 102399999 1034240 505M 27 Hidden NTFS WinRE
/dev/sda4 102400000 234440703 132040704 63G 5 Extended
/dev/sda5 102402048 103426047 1024000 500M 83 Linux
/dev/sda6 103428096 234440703 131012608 62.5G 83 Linux

Disk /dev/sdb: 931.5 GiB, 1000204886016 bytes, 1953525168 sectors
Disk model: HGST HTS541010B7
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes
Disklabel type: dos
Disk identifier: 0xf1528e22

Device Boot Start End Sectors Size Id Type
/dev/sdb1 * 2048 206847 204800 100M 7 HPFS/NTFS/exFAT
/dev/sdb2 206848 104857599 104650752 49.9G 7 HPFS/NTFS/exFAT
/dev/sdb3 104857600 1953523711 1848666112 881.5G 7 HPFS/NTFS/exFAT

Disk /dev/mapper/rootfs: 62.5 GiB, 67061678080 bytes, 130979840 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes

Disk /dev/mapper/veracrypt2: 881.5 GiB, 946516787200 bytes, 1848665600 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes
Disklabel type: dos
Disk identifier: 0x6e697373

Device Boot Start End Sectors Size Id Type
/dev/mapper/veracrypt2-part1 1936269394 3772285809 1836016416 875.5G 4f QNX4.x 3rd part
/dev/mapper/veracrypt2-part2 1917848077 2462285169 544437093 259.6G 73 unknown
/dev/mapper/veracrypt2-part3 1818575915 2362751050 544175136 259.5G 2b unknown
/dev/mapper/veracrypt2-part4 2844524554 2844579527 54974 26.9M 61 SpeedStor

Partition 1 does not start on physical sector boundary.
Partition 2 does not start on physical sector boundary.
Partition 3 does not start on physical sector boundary.
Partition 4 does not start on physical sector boundary.
Partition table entries are not in disk order.