Why is the SSD behave so poorly in the upper bay

hi there,

I wanted to replace my stock 1TB hdd (Mac Mini 2012, i7) to dual drive: HDD + SSD. When both mounted in the mini OSX wanted to format them into a fusion drive, which was not what I wanted. Therefore I unplugged the HDD and only left the SSD in an upper bay (farther from the bottom opening).

I had several problems formatting it. Installing the system took around 9 hours, after each reboot it took several mins to get rid of the "prohibition sign". Finally decided to install the yosemite using mini in target mode, then installation was a breeze.

But after booting up the Mini with this installed system i took about 15 minutes to boot. I could move mouse, drag windows but each action, each click that involved disk operations caused a minute of the "beach ball".

I decided to put the same drive, with the same system installed, onto the lower bay - the one closer to the mac mini bottom case. It launched like a rocket, system starts within 10 seconds, and is really fast.

QUESTION:

Why is this SSD so slow in the upper bay and behaves fine in the lower one? Is it possible, that the sata cable is damaged in some way? I dod not use it before. The disk, however, behaved rather normally when I used it with target mode.

Can I try to install the HDD now in the upper bay with that cable and expect it to work fine? I am little afraid mounting and dismounting the mini back and forth. Or better leave it like this, while everything is working fine?

Thank you all for the replies;

DAN: really I would like to have both the SSD and the HDD connected internally in the MINI, provided that that does not slow down the machine. I mainly use Logic Pro for music creation, second drive could serve as backup and data bank then. Now I just have the HDD connected via USB 3, which is also fine. The screenshots:

the SSD, in the lower bay:

Intel 7 Series Chipset:

Vendor: Intel

Product: 7 Series Chipset

Link Speed: 6 Gigabit

Negotiated Link Speed: 6 Gigabit

Physical Interconnect: SATA

Description: AHCI Version 1.30 Supported

Crucial_CT512MX100SSD1:

Capacity: 512,11 GB (512 110 190 592 bytes)

Model: Crucial_CT512MX100SSD1

Revision: MU01

Serial Number: 1XA10E3E66FK

Native Command Queuing: Yes

Queue Depth: 32

Removable Media: No

Detachable Drive: No

BSD Name: disk0

Medium Type: Solid State

TRIM Support: Yes

Bay Name: Lower

Partition Map Type: GPT (GUID Partition Table)

S.M.A.R.T. status: Verified

Volumes:

EFI:

Capacity: 209,7 MB (209 715 200 bytes)

BSD Name: disk0s1

Content: EFI

Volume UUID: 0E371BC6-F160-3309-89CF-1C11F78AF46B

SSD:

Capacity: 511,25 GB (511 250 432 000 bytes)

Available: 357,31 GB (357 305 466 880 bytes)

Writable: Yes

File System: Journaled HFS+

BSD Name: disk0s2

Mount Point: /

Content: Apple_HFS

Volume UUID: 5111A182-F70D-3A6C-B159-AD7ABBC3DBF7

Recovery HD:

Capacity: 650 MB (650 002 432 bytes)

BSD Name: disk0s3

Content: Apple_Boot

Volume UUID: FA9BF509-0E1A-112D-95BD-0C433DC68AE6

the HDD in an external enclosure connected via USB 3:

AS2115:

Product ID: 0x1153

Vendor ID: 0x174c (ASMedia Technology Inc.)

Version: 0.01

Serial Number: 00000000000000000000

Speed: Up to 5 Gb/sec

Manufacturer: ASMedia

Location ID: 0x15100000 / 2

Current Available (mA): 900

Current Required (mA): 0

Capacity: 1 TB (1 000 204 886 016 bytes)

Removable Media: Yes

Detachable Drive: Yes

BSD Name: disk2

Partition Map Type: GPT (GUID Partition Table)

S.M.A.R.T. status: Not Supported

Volumes:

EFI:

Capacity: 209,7 MB (209 715 200 bytes)

BSD Name: disk2s1

Content: EFI

Volume UUID: 0E239BC6-F460-3107-89CF-1C97F78AB14B

Untitled 1:

Capacity: 999,86 GB (999 860 912 128 bytes)

Available: 776,02 GB (776 017 113 088 bytes)

Writable: Yes

File System: Journaled HFS+

BSD Name: disk2s2

Mount Point: /Volumes/Untitled 1

Content: Apple_HFS

Volume UUID: 831331D1-47B7-3DAF-840F-AA433DB3247A

that's some... HGST, SATA, 5400, type TS5SAF100,. the stock drive i guess